For convenience, I have always purchased a set of removable saddlebag and tour-pak soft luggage. While staying at motels or even while camping, it so much easier than going back and forth to the scooter because you forgot something.

 

Like many of the others have said, keep the heavier stuff in the saddle bags. Stuff you need access to during the ride is good to carry in the Tour Pak. I like to leave room in the Tour Pak to lock up my helmet, gloves and glasses, etc if I stop along the way to eat or shop.

 

+1 on the Bag liners. They sure do make loading/unloading simple, especially if it's raining!
Everyone else pretty much covered it too. You'll find your own methodology the more you tour.

 

we use some beach bag type bags that fit in the saddle bags, one side for me one side for her, the tour pac we keep a collapseable ice chest (small one) for luch meat, mayo, couple of drinks ect. also jackets, maps, and misc. stuff. i have a small tool bag i squeeze into my bag and off we go.