[jhautz]

I would balance the cells as a set if you are going to run them as a set. You need to make up a balance harness to balance both packs together. Refer to BrianGs rc calculations website. It has a great diagram of how to do it.

As for discharged batteries. You can leave them for a little while with no issues. I wouldnt go more than a few days or so though. The batteries do slowly self dicahrge over time. Not a fast as the older NiMH cells, but they do still slowly discharge. If you are the bottom limit for the cell and leave for an extended period of time you could theoretically let them drop too low. But, Its not like you need to run them to the charger right away or anything.