The ideal way to do rust repair is...number 1 and foremost...strip the car. If you don't take all the existing paint off, you could be and in all probability are painting over some areas that are rusted. When the car is stripped, rusted areas that where covered by old paint and will come out after the car has been repainted.
Rust should be cut out and a patch welded in. The patch panel should be made of the same thickness of steel as the rest of the body...in your case I believe it's 22 gauge, but, I'll double check to be sure. Where you have rust, you don't just cut the rusted area out, you need to remove enough metal around the rusted area, look at the back of the metal to make sure that you have all the rusted area removed and have sufficient metal to weld too. After all the rusted areas are looked after, several coats of Epoxy primer need to be applied (it is also possible to prime the car with Epoxy primer 1 panel at a time, that way you minimize surface rust on initial panels that had been worked). Then you apply filler, we can get into the ways of applying filler when we get to that point. After the filler/body work is done, the whole car gets re-primed and block sanded until it is perfectly straight. Then the car is painted...simple right...no...there are many things that you will learn and it is anything but easy.
That covers methods to a point, every situation may require a different method or technique which will be covered at the appropriate time. As far as materials, it's a long list which I will give you in the form of a Private Message...(Not because I don't want to do it here but I'm getting tired, it's almost 12:30 AM where I am and I have and early meeting in the morning)
When it comes to tools, I would like to know what you have available and will give you a list to look for in the PM.