When going for a cross, do i begin charging on the opposite side that i am jumping from?
You might as well. It’s technically possible to do stuff like crossup -> charge ultra but it’s prohibitively hard because you have to switch from one direction immediately to the other on the exact frame that your character switches sides. Therefore you can’t really save the charge from one direction.
Yup, although it’s fairly difficult to land any kind of combo that requires a back charge. But if you intend on using a special move that has a down charge, just simply hold one of the ‘down’ directions while you do the crossup, and you’ll have plenty of time to charge it.
As far as charging ‘back’ motions, just charge back as you jump, then once you cross to the other side of them, charge the other way. If you land the combo, you might need to throw in a few light or medium attacks before using it, in order to give yourself enough time to charge.
Like eltrouble said, charge characters have BnBs off a crossup that don’t require back charge because of this. You either go into another special (For Honda, Chun, and Blanka, that’s probably their mash move) or you make the combo long enough to build enough charge. Bison can do something like cr.lp s.lk cr.mk xx scissors after a crossup if you just hold the other way.