I do the leg over thing, but instead of over the seat like normal, I scoot up to the stem and intentionally bend my leg as much as possible.
As for the kickstand thing, we've never had issues with the Kickback on the Xtracycles during loading/unloading. Even now I only have the single on my Xtra and I can still get my daughter on/off without holding the bike. Granted she's five now and knows to shift her weight until I get rolling; that may not be the case with your son.
The weight is a little weird at first, but you quickly get used to it and how to "feel" the bike when he's just moving around or when you're really off balance.