Some pictures would go a long way. The spot above the windshield if it's as you're describing it, is probably surface rust and the result of a rock chip. If it doesn't go under the windshield molding it's pretty straight forward, sandblast the spot with a small handheld spot blaster (you can get these for about $20, you'll just need some sand and access to a compressor) then put some epoxy primer on it, putty, sand, high build, sand, paint. (if all you care about is preventing rust and aren't worried about looks you can simply epoxy and then paint over top) If it's under the windshield you'll have to pull it, do the work and either put the glass back in or replace it if it's broken or breaks on the way out.
The other spot, it's pretty hard to give accurate advice without seeing it. Everyone seems to think they have surface rust, occasionally it is, usually it's the panel has rusted through from the back and now it's starting to show through on the outside.