Rust, as you probably know, is the bane of this car. Generally the rust you see is about 1/4 of the rust that actually is present, so it is critical to deal with the problem quickly.

You mention a spot below the glass that has rusted. If this is the area where the rubber seal rests, the rust is usually because the two tiny drains in that area are blocked. You need to remove the seal, clean out the drains, then fix the rust. If the rust is minor and hidden by the seal, I would just grind it to bare metal and prime and paint. Or, if you want to be more aggressive you can order a product called POR that will keep it from ever rusting again. If the rust is beyond the seal or has made holes in the metal you really should put in new metal. You can do this yourself with a wire-feed welder if you feel brave or have the expertise. Other options, though less reliable, are to cover the holes with metal that is held in with pop-rivets or to cover them with a good fiberglass-type body filler. Most body fillers you get in the local chain parts store won't work well for this application because they actually absorb water. An automotive paint store should have a better product if you decide to go this way.

The rust at the bottom of the doors is likely from the same cause. The doors (and the sills below the doors) have small weep holes to allow water to drain out. They are easily blocked with dirt that accumulates over the years. The fix is the same. In this case, though, the rust is likely coming from the inside out. You want to remove the inner door panel and treat the inside bottom area of the door thoroughly.