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You can fix the rust spots if they haven't rusted through. The trick is to do it so they won't come back. You have to kill all of the rust underneath the paint. Sand the spots down to bare metal out maybe a half inch or so beyond the rust. Then use a rust converted or POR-15 to cover the entire area. When that dries sand just a little more with something very fine like 400 paper, tack if off good then cover it with a good primer and finish with the top coat feathered in carefully. That should keep the rust from recurring. While you're at it be sure all the drain holes in the panels are open so any water that gets inside the door or fender panels can drain out and the inside can dry out.
Hope this is some help.
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