As it has been stated you won't have to worry about the corrosion penetrating all the way through and actually causing leaks or anything like that. And if that does happen, just send me some pictures and we will send you a new system.
My recommendation for painting the exhaust would be lots and lots of newspaper. If you decide to paint the parts on the car then just line the underside with news paper. Don't worry about the newspaper being really pretty or anything like that. It's only going to be on there for a little while. I've masked off roll cages and what not in the past and the important thing is making sure the area that you're painting has plenty of area around it for you to paint and that anything you don't want painted is covered up. It really doesn't matter how pretty the masking job is since it's only going to last a few minutes.
One thing to keep in mind is that you will have to deal with some overspray if you don't do a really thorough job of masking. If it were me, I would simply remove the exhaust from the car and re-install it later. The finish will be a lot nicer and the overall time will be a lot shorter.
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