Sorry mate, wouldn't have the foggiest! Never had a dual swingarm before haha.
However, my mate used to put the rear on a paddock stand (leave the front on the floor) and stick a spirit level between the wheel resting ontop of the seingarm. He would then adjust the wheel until the wee bubble ended up between the lines. Not exactly thorough but the wheel was aligned!
As for chain tension, I always tell people that when sat off the bike, the chain should have around 1" of play. However, it does cary from bike to bike. So check the service manual.
If you feel you MUST sit on the bike, put the bike on the paddock stand, lay on the seat (plank style) and lean over. Grab the paddock stand and pull your self down to it. Check the chain then, if there is no flex at all, you will snap it at some point!