I would be careful with running lipos in parallel. If you do try and always run the pair together, and check before and after for any signs of damage, specifically the packs puffing up, or dead cells. While for the most part you will likely be fine, lipos are really temperamental and running them in parallel, is not exactly the “professional” solution. The concern with having each battery power one motor is that as the battery voltage is depleted the power may become unequal between the motors, and your controller may have difficulty staying on a straight path. The ideal way would be to use a merge circuit which draws from the battery with the highest voltage, but if you take care to keep the pair together and with the same capacity, voltages and brand you should stay fine if you are careful.