Fiducials are used by the pick and place machine to provide better accuracy when placing components on the PCB. There is a camera that recognizes the fiducials and uses it as a registration point to calibrate where the machine thinks it is on the PCB.
There are two types of fiducials: Global and Local.
Normally a PCB will have 3 global fiducials per side (top & bottom), and usually in the corners of the PCB. This is so it can recognize the boards overall orientation and position.
Local fiducials are located near some of the critical parts. Usually there are two fiducials for each part, in opposite corners. IF you have several critical parts that are close together then a fiducial can be shared by two or more parts-- reducing the number of fiducials required and the the PCB space taken up by them.
Where you need local fiducials really depends on the pick and place machine that will be used, and the placement accuracy required by the component. Chips with a finer pin pitch will need fiducials more.
It's interesting to note that TQFP's need fiducials more than most BGA's. Most TQFP's have a pin pitch of around 0.5mm, while most BGA's are 0.8 to 1.27mm. BGA's also have a cool ability to somewhat self-align due to the surface tension of the melted solder. But I need to stress that this is very component and machine dependent, so check with your assembly shop.
Also machine dependent is going to be the construction of the fiducial. Things like how big the pad is, and how much the soldermask is pulled back. Usually the fiducial is round, but sometimes square or bow-tie shaped.
Another thing is that some assembly shops will request fiducials to just feel good about things-- but don't really need them. My second to last PCB had had lots of fine pitch BGA's, QFN's, and TQFP's and had no fiducials on it, but there were no issues with parts placement. My current board is nowhere near as difficult but they are requesting fiducials. Go figure. I'll humor them and put the fiducials on it.
To be honest, I don't see any problems, though I have read the question twice now.
I don't even see any problems soldering the RTC, as an SO8 package really isn't that small, even for a hand made PCB. What's your PCB production method?
To maintain good accuracy, you might consider keeping the circuit at a controlled temperature. You could use a Peltier element plus a thermistor to regulate the temperature.
There are such things as temperature compensated oscillators (TCXO) and Oven Controlled Oscillators (OCXO), but these don't seem to be available at 32.768kHz.
Best Answer
You can, its really great for breadboard wire. I used to use Ethernet or phone as my primary way to prototype (now I only solder).
A better way is to use the standard "blue wire" 30AWG for jumper connections, its smaller so it's easier to attach to most SMT pins.
There are some caveats with solid core ethernet wire though, The main problem is strain relief and breakage. As with any wire, stripping can nick the wire, and the wire breaks after moving. This is especially a problem if the wire is causing intermittent connections, it can be hard to track down.
So be careful not to nick the wire, and if you can, provide strain relief with tape or soldering. Don't move the wire after it is placed.
(you should also not use solid core ethernet from the wall to the computer, if it's stepped on it breaks, and if it's moved too much it breaks, use stranded instead)