Hi kydra1.
The thing to realize here is that when you do this you half the voltage to charge your cells but you must then supply double the current to charge them.
If you have two 3.6v 2000mA cells in series thats 7.2v 2000mA
Those cells wired in parallel are 3.6v 4000mA.
Charging off a solar panel on series takes 2 hours (for example) charging in parallel requires a panel with double the amperage or takes twice as long. (This does not make one pannel cheaper than the other)
Not to mention that while doing all this you must run the Arduino off another power source.
Or set up your battery system to run the arduino then get a pannel able to charge the batteries while they are running the Arduino.
Have you worked out what your system needs? Eg. Volts/Amps to run.
Without that you have no idea of the battery capacity or the pannel required to charge it.
If running a system from rechargable batteries with solar charging dont forget to factor in the cost of readily available parts (cheaper) at apposed to not readily available parts (more cost).
For example a 12v 4Ah Sealed Lead Acid battery with a controller and pannel then a buck converter from 12v down to 5v would probably do what you want.
You need to allow for the battery to be able to run the whole project for three days with no sun(charging) and the pannel should be able to supply enough current to charge the battery in as little as 6 hours of sunlight to ensure continuous running.
Daz