In theory yes, you can put batteries in parallel, but problems arise if the two cells are not identical. In factories where this is done to construct battery packs, the cells are chosen to be similar.
Yes, I should have added that the worst thing that happens is that the life of the combined cells may be less if the cells are not well matched. This matters for laptop battery packs for instance, but maybe is not so critical in your application. I agree with Georacer - you can go ahead as long as you take some care to match the cells as noted.
If you are going to be putting 2 Lipos in parallel then make sure they are the same capacity , brand etc. Also make sure they are both charged up at the same level.
You probably know this , i'll say it just in case you don't :
Lipos need special Lipo chargers and if they go above a certain voltage per cell then they can catch fire etc and if they go below 3,0 - 3,2 volts per cell then they die with no chance of recovery.
Generally it's good not to let it drop lower than 3,4volts per cell and not higher than 4,2 volts per cell
Just be carefull , Lipos aren't very forgiving and can catch fire if not handled properly.