Edited 2017 - changed recommended long life storage voltage and added comments on fast charging using some recent systems. RM.
What YOU do as regards several of these questions depends largely on what YOU are trying to achieve or test.
Discharge to cutoff is fully discharged (to whatever remaining % that voltage represents). That's the easy one :-)
Percent dropoff of current in tail sets final % of max possible charged reached. There was a superb table given here within last week or so. Can supply later if you don't find it.
Real Men™ plateau at 4.2V and tail down to 10% or even 5% of the constant current rate. This gets the battery full and knocks the stuffing out of it.
Others terminate the current tail at say 25% of cc value.
Optimum lifetime for ongoing usage is at about the end of the constant current phase. That makes it very easy to locate - charge at specified current until desired max voltage is reached, then charge at constant voltage as desired. Here "desired" is to stop immediately. This is the point at which batteries tend to give significantly longer whole of life mAh of storage without grossly reducing mAh capacity per cycle. This is liable to be the point where older "fast chargers" tell you they have finished. Actual % total claimed varies but probably 70% - 80% range.
Newer USB input fast chargers use the term differently. In the case of USB the maximum available charge current at 5V is 5A so that the battery MAY be able to be charged at ~= 6A for the CC part of the cycle using an efficient buck converter to drop voltage and raise current.
[For a buck converter: Vout x Iout = Vin x Iin x efficiency_of_conversion]
Some systems such as QuaqlComms Quick Charge system allow the use of higher charger voltages (9, 12, 20) with specifically designed equipment, so battery charging can be faster for a given voltage provided that the battery specification allows this.
Maximum charge rates for LiIon and LiPo batteries are usually C/1 = 1A per Ah of battery capacity.
At 5V, 5A a USB charger can charge a 6000 mAh 1 cell LiPO battery at max rate - so eg a 10,000 mAh single cell battery used in some larger tablets can not be charged at the allowed 10A ! rate.
For long life storage where actual stored capacity is unimportant, LiIon and LiPo cells should be stored at about 3.7V.
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Using cells without protection adds to the rich tapestry of life. As long as you don't mind the occasional scorch mark on the tapestry that's fine. Note that part of the protection is a one time high capacity fuse under the cap for when things get out of control. Undervoltage discharge destroys. Charging from below a certain voltage at full rate can get fun, I'm told. Charging at reduced rate can bring cell up, I'm told. Below another second level they say don't even think about it. I've had very poor success in trying to get LiIon to misbehave. I have a box of unprotected cells that are very uncooperative about venting with lame etc. Strange. Sony and Apple and even HP seem to be much better at it :-).
What colour is the magic smoke when it vents with flame ? :-)
Rushing immensely, more later, but ...
What you describe seems to run a severe risk of doing damage.
To be ure, first you need to specify the allowed MAX charge rate for each LiPo.
You have 1.0 + 1.2 = 2.2 Ah in parallel so 5A = 5/2.2 = 2.27C.
This MAY be OK if cells are specd as 2C or more and are balanced in draw.
If specd at say 10C then it all may survive.
If specd at 1C it is very very bad.
BUT when a cell pair plateaus at 8.4V it's current will start to drop and if the charger is able to make 5A the extra current WILL flow into the still in current more other battery pair.
If max charge rates are not >> 2C then what you describe is at best an extremely poor compromise and at worst a disaster either in magic smoking or in cell lifetimes.
If max charge rates are around 2C then what you describe is at best a beating of some of the cells regularly and at worst a journey towards magic smokedom.
In an arrangement like this with different capacity pairs wired in parallel you need to carefully monitor individual cell pair or even cell voltages to prevent discharge-damage. This is going to make balancing more important, although I have been impressed with how well cells from the same batch seem to track when I have checked it (not often).
Operating cells of different capacities in parallel is an immednsely bad idea usually unless you manage and turn off each pair individually.
Apart from one pair endpointing before the other and throwing more charge or discharge onto the other there is a lack of certainty re how cells load share.
eg Say you have a 1000 and 1200 mAh cell and load both with 1000 mA. The large cell will see this as less of a percentage load so it's natural terminal voltage will be larger and it will "happily" supply the extra current. but there is no guarantee that it will o this in the ratio of the tywo capacities. The large cell may prove very "sacrificial and provide most of the load for most of its capacity. BUT when it finally falters the small cell will then take up most of the load and may now be overloaded. And there is no certainty that the LARGE cells will not now expire and be driven into a damaging mode. Probably not, but. too many uncertainties.
Why run cells of different sizes and in this 2 x 2 pattern?
Key question: What are the max allowable charge current rates for the 1000 and 1200 mAh cells.
Without this information the question become svery hard to give a good answer to.
Best Answer
I can help with a different POV as I have Bottom Balanced for several years.
Let's clear up one thing quick. You do not give up or do away the Balance Leads. They are still used to monitor things time from time. Jus tnot used for charging.
OK start with a different POV with a Stupid Question. What is the capacity of a battery when at 100% SOC? You cannot answer the question. Next Question. What is the capacity of a battery at 0% SOC. Easy answer, 0 AH for any battery or type.
LiFeP04 charge and discharge are very flat, and you cannot determine the SOC from voltage. Only place where SOC is accurate is at the 0% SOC or Bottom (2.5 volts), and 3.65 volt at 100% SOC. Capacity at 25 vpx is 0 AH, and at 3.65 is unknown.
So what is the capacity of a Bottom Balanced pack charged with 90 AH. It has 90 AH each and every cell. All cells will reach 2.5 volts at the same time, thus eliminating over discharge. No cells in a series string will have any energy left to drive weaker adjacent cells to reverse polarity thus destroying it.
When you buy say 100 AH Prismatic Cells, the capacity of each cells varies -5 to + 10%. That means the weakest cell can be 95 AH, and the strongest 110 AH, a 15 AH distance. So say you make a 8S pack, and Top Balance. What is the capacity? 95 AH right? Sure you have cells with more than that, but to use it means you would have to drive the weaker cells into reverse polarity and destroy them. When you charge the cells to 100% SOC just means they are 100% SOC and not squat about capacity. Capacity is determined by the weakest cell in the chain.
Nothing destroys a lithium battery faster than over discharge. Not much a problem with other chemistries, huge problem for Lithium. Right now your mind is stuck in a box; Thou Shall Fully Charge My Battery.
That is a sure fire way to destroy Lithium Batteries. Change the charging strategy and logic. Start from a know point of knowing both Capacity and SOC which is at 2.5 volts = 0 AH capacity. Now wire the batteries in series and charge until the first cell reach roughly 3.7 volts and terminate charge. Note voltage, AH input, and which cell shot up to 3.7 volts very quickly at termination.
Example 95 AH went in, on a 8S LFP pack the voltage was say 27.1 volts, cell 3 went high. You know now you have a 95 AH pack and need to set charge voltage to just slightly less than 27.1 volts.
When Bottom Balanced if you discharge too deeply, no cell is destroyed, they all hit 0% SOC at the same time and the voltage collapses from 11 volts to useless in a few seconds. In a Top Balanced system one cell will be fully discharge before any others, and can be destroyed byy adjacent cells if not caught very quickly.
There is one more huge benefit from Bottom Balance. Double to Triple cycle life. By limiting SOC to less than 100% adds cycle life. Limit to 95% SOC on the charge cycles, and limit discharge to 90% DOD, and you get Double to Triple cycle life. All you gotta do is get out of that Thou Shall Fully Charge My Battery box you are trapped inside of.
Why is Top Balanced used commercially? Two reasons. Consumers are idiots and cannot be trusted. Sure enough some idiot will burn something up and look for deep pockets. 2nd reason is it is very easy to design and build Top Balance Chargers. It generate up sales, and shortens battery life which is good for the manufacture. Stupid Consumers will never know.
Bottom Balance takes skill and understanding of what is going on. Use the Balance Leads to check voltages from time to time. Do a full discharge test every 100 cycles and check Balance.