assuming you just use a Y cable for the battery packs, then they both run in parallel all the time.
Two packs with equal number of cells will also be paralleled if they are just plugged into any two open slots in the Rx. This would be the first choice over using a "Y" connector. The packs will drain fairly equally and if one should fail the other will keep things working as normal. It's also important to use two separate switches/charge receptacles.