In my experience, the shape of the ninjette's tank makes a big magnetic tank bag kind of hard to fit. I'd get a smaller tank bag that fit the shape of the tank for things like your sunglasses, wallet, keys, gloves, etc. and then get a tail bag that wraps around your back seat to put your bigger stuff in.
I'll second what you said though, after about 45 minutes of riding with my backpack on my hands start to go numb from the straps putting so much pressure on my shoulders. BTW, that's with a good "hiking" style back pack that was made specifically for riding. One of the ones that have both a waist band and a strap across your chest to try to relieve some of the pressure off your lower back.
It's a trade off, the convenience of the backpack is nice, get off the bike and take your stuff with you, but it's not really all that comfortable and here in the south, you'll bake in the summer when you wear it.
Also, as a side note, be careful with magnetic tank bags and inspect the bottom of them before you put them on the bike. They pick up metal really really well. I've found staples and paper clips attached to the bottom of mine on many occasions and I'd hate to see what that'd do to the paint on your tank after you slide it around to get it positioned right.
