Seen it done both ways - charged together and charged separately. Charging is not the prob - you just use same parallel connector that you use to run them in parallel.

Balancing is the issue. For charger to 'see' all the individual cells, they have to be in series. You can charge them in series and balance them this way, then run them in parallel as you want to.

As long as the lipos start off close together charge and balance wise, there shouldn't be any probs.