Nope, you are escentually charging one big 2S battery. At least as far as your charger is concerned.

It will see 2 cells and the same voltage as if it were just one two cell battery. What will change is the charge current because you doubling the mAH.

It's only the, for lack of a better term, "volume" and hence charge current that will change. For example, assuming you don't have a charger that will do the math for you ( you should get a good charger and Para board if you intend to parallel charge); assume you charge two 2S 4100mAh batteries in parallel.

A 1C charge rate would be 8.2 amps at full charge voltage would still be 8.4 volts. The charger would charge the battery as if it were a 2S 8200mAH battery.

IMHO if you're going to do much parallel charging you should invest in a very good fuse and thermo protected parallel charge board and a high end charger. Especially given what seems seems to be prep city to abuse LiPo batteries in the the RC car hobby.

Something along the lines of a PL6 and FMA (or similar) board for instance.

Take a look at buddyrc.com or progressiverc.com for higher end chargers and para boards.