HELLO!
An answer to some of your questions-
1. Batteries can be charged and stored horizontally. We have a charging station in which the batteries are slide under the chargers. Just note that when horizontal, the terminals will have a larger chance of getting smacked around/damaged. We store ours vertical but whatever works out for you.
2. Multifunctional crates are allowed, but don't go making your crate just yet, FIRST most likely is going to change the size of them for this upcoming year so waiting until kickoff to build your crate would be a good idea. More info on the crates can be found here-
http://usfirst.org/roboticsprograms/...70&terms=crate