The confusion here is from the initial poor description of how a battery works.
A battery consists of three things: a positive electrode, a negative electrode, and an electrolyte in between. The electrodes are made of materials that strongly want to react with each other; they are kept apart by the electrolyte.
The electrolyte acts like a filter that blocks the flow of electrons, but allows ions (positively charged atoms from the electrodes) to pass through. If the battery is not connected to anything, the chemical force is pulling on the ions, trying to draw them across the electrolyte to complete the reaction, but this is balanced by the electrostatic force-- the voltage between the electrodes. Remember-- a voltage between two points means there is an electric field between those points which pushes charged particles in one direction.
When you add a wire between the ends of the batteries, electrons can pass through the wire, driven by the voltage. This reduces the electrostatic force, so ions can pass through the electrolyte. As the battery is discharged, ions move from one electrode to the other, and the chemical reaction proceeds until one of the electrodes is used up.
Thinking about two batteries next to each other, linked by one wire-- there is no voltage between the two batteries, so there is no force to drive electrons. In each battery, the electrostatic force balances the chemical force, and the battery stays at steady state.
(I kind of glossed over what it means for two materials to "want" to react with each other. Google "Gibbs free energy" for more details on that. You might also google "Nernst equation.")
My favorite educator, Bill Beaty, often rants at the many misconceptions that all too many people have been infected with.
One of the many common misconceptions involves batteries.
"Frequently-Asked Electricity Questions":
"THE LIQUID BETWEEN A BATTERY'S PLATES IS A GOOD CONDUCTOR.
SO WHY DOESN'T IT SHORT OUT THE BATTERY?"
"Why is electricity so hard to understand?"
"...mistaken belief that no charge flows through batteries. ...
This leads to the traditional incorrect flashlight-current explanation (current comes out of battery, flows...etc.)
It also leads to the misconception that batteries
SUPPLY CHARGE, and have a storage place for "used" charge.
This might make sense if we believe that there's no path for charge through the
battery.
But it's wrong, because there is a path, a path provided by
flowing charged atoms.
Charge must flow around and around a circuit,
passing THROUGH the battery over and over."
"But how SHOULD we teach kids about 'electricity'?"
"A battery is a chemically-fueled charge pump. Like any other pump, a battery takes charges in through one connection and spits them out through the other. A battery is not a source of the "stuff" being pumped. When a battery runs down, it's because its chemical fuel is exhausted, not because any charges have been lost. ...
When you "recharge" a battery, you are pumping charges through it backwards, which reverses the chemical reactions and converts the waste products back again into chemical fuel."
'Which way does the "electricity" really flow?'
"When you connect a lightbulb to a battery, you form a complete circuit, and the path of the flowing charge is through the inside of the battery, as well as through the light bulb filament. Battery electrolyte is very conductive."
Best Answer
In the simple series connection, the current will be limited to the current from the battery with the lowest current rating. Note: that may not be the smallest of the batteries, either in physical size or in total energy storage. Just for example, Nickel-Cadmium batteries generally have very low internal impedance, so even a fairly small NiCd battery usually has quite high current capability (but will discharge very quickly at maximum current capability).
When batteries are connected in parallel, you add together the current capabilities of the batteries.
For your series/parallel connection, you'd want to connect at least enough of the smaller batteries in parallel in match the current of the larger battery (or at least to match the current requirements of your circuit). If you connect more in parallel than that, you'll get the same total current flowing, but less through each individual battery, so they'll discharge more slowly. That'll give longer battery life unless current draw is so low that the batteries are already limited by their shelf life (which is unlikely where they're powering motors and such).
In most cases, however, you want to ensure that any batteries you connect in series are as close to identical as possible--regardless of overall current capability, if some of the batteries discharge at different rates from others, things can get fairly ugly.