My observations, and several discussions with Mike and Kurt of Fromeco:

If you run two straight packs into the RX, the cross charging is really negligble because the higher voltage will cause current flow mostly into the RX until it drops down to some nominal value. Its kinda like two cars going down the road at the same speed approximately... they both get there nearly the same time. the difference is not important unless racing..

Add regulators to the mix and things change dramatically:
IF you have two Batts and two regs wired directly into a common bus with no battery sharing circuitry, almost every time, one regulator will be at a slightly higher voltage. That battery provides most of the power except during high demand points. I have done it over and over in bench and flying. My nano has twin regs. I cannot get them closer than .1 volts together, so one battery drains 75% before the other really gets draining. Moral: you must check both batteries. You should learn the characteristics of each setup you do or it will eventually bite you.

If you have some sharing circuitry, it will normally allow the batteries to draw down together. Enter the wolverine, the smartfly, the weatronics..... PB switch...etc... THis gives another level of insurance if that is what you like. My preference is this setup. I use wolverines, or receivers with sharing technology built in. such as JR batt safe rx.

Batteries:
Lions internal resistance allow you to pull them down with less load, thus the 7volt/1amp Rule of thumb. This does not work for any other chemistry. Andy Low has come up with an A123 checker, but before that we checked them unloaded. 6.2 was my minimum, and that was really min.. The only true answer was to know how much the plane used in MAH and never push it past 50% usage. I still live by that rule. the one time I pushed it, I lost a plane because I did infact have a bad cell. If you run A123's you must balance them...there are hundreds of posts as to why, just do it... they actually are more prone to unbalancing than lipos are when used in a very low current setup (receiver packs). Finally Lipos. Like A123's, they have low cell resistance but higher overall voltage, so the ION rules dont apply to them. Jack is right on with the statement about less than 50% remains if you use a ION checker with them. the problem is that its really east to overtax them at low charge state, and with regulator losses factored in, I can see fadeouts happening, so oversizing them is good since they dont weigh alot. I think battery sharing circuitry is the most important running a Lipo.

With todays balancing chargers, you have to learn what each setup uses and how your packs act in each setup. So fly twice, charge....fly twice...charge... see how much you put back. round up to the nearest 100Mah, and then never go past 50% capacity MAH used..

I know some of that info is repeated here but .. thats my 2c for what its worth...

It goes up from there, but that is the basics in my opinion on managing power