Hi im not a battery expert but seeing as no one else replied I will try and offer a little advice.
Info seems to suggest it is bad to discharge below 2.8/3.0v under load and charge more than 4.2 will shorten the battery life. 4.25v being the absolute safe maximum.
So if you charge to 4.2v the maximum difference would be 50mV, although that doesn't sound much I tried discharging a pair of cells in series a few times and the voltage difference between the cells stayed so close I could hardly measure it, around 1mv I think it was.
To balance, charge them up individually then leave connected in parallel for a few hours to settle, then build into series circuit.
It is good that you have used protected cells, second I hope they are quality from well known manufacturer like sanyo, LG etc, I have used these cheap ultrafire/trustfire batteries and although I haven't had any problems, the capacity was much lower than stated and internal resistance quite high, also there are safety mechanisms under the positive end and cheap cells might not have those, cheap cells are a disappointment eventually.
If you start with a balanced pair of quality same age cells in series in normal use they will stay balanced for a long time with no attention, high discharge rates might make them become unbalanced faster though.
For curiosity what is your discharge current, some protection circuits can cut out as low as ~3.5 amps apparently,
18650 batteries are amazing in their capacity and light weight but not as robust as the old ni-cd cells which I still have an strange affection for.. Also I don't think they suffer from Peukert's law,
Peukert's lawMaybe someone else can offer more advice than this novice.
They are very safe batteries when used with respect. Have fun.