Sharing negative terminal ("ground") between 2 LiPo batteries and UBECs / paralleling 2S LiPo packs
I don't have time to answer your whole question, but probably the most important part is regarding the batteries. Putting the the batteries in parallel is OK if they are the same capacity and age and the same charge when they are put together. 

Simply connect positive to positive and negative to negative and you are done. You do not have to take them apart to charge them. They will immediately balance as they charge with respect to being in parallel. The batteries in series still need to be balanced. You can consider the two batteries that you have connected in parallel as just one larger capacity battery and then continue with your project and make your connections as needed. 

Hope this helps.