Barry has valid points that will serve you well, do one rust repair at a time, for exactly the reasons Barry gave you. Start with the smallest one first, make your repair panel fit properly and weld it in using a stitch method, allow each weld to cool before attempting another one and stagger your welds (weld one spot and than the next one as far away from the first one as possible). This way you will minimize the warping of the metal you are welding. All welds must be closed, by this I mean when you are done welding there shouldn't be any gaps between welds, it should look like one continuous weld. Grind your welds down with a disc, no coarser than 36 grit and 50 grit works also. Rough up the metal around your repair area with your grinding disc and apply your body filler. Block sand your body filler, starting with 40 grit, moving up to 80 grit and finishing with no less than 180 grit before priming. You can guide coat your body work so that when you block it for straightness, your low spots will show and you will be able to apply more filler to the low spots. When you prime, prime and area well beyond the repair area, apply a second coat within the first coat and a third within the second coat allowing each coat to flash before adding another one.
Now you can move onto your next larger rust area. The experience you gained by doing a small area will serve you well when attempting a larger area.
It doesn't really matter if you strip the car first or do rust repair first...I would do rust repair first, especially if you may need to move the car in and out, you don't want to expose the car to the elements considering it would be in bare metal. When you strip a car there are several ways to go about it, you can use 80 grit on a DA (dual action orbital) set on the rotating only mode. If this is the way you plan on going, keep your paper fresh and sharp and keep the orbital moving at all time. If the paper isn't sharp or you spend to much time in one spot with your orbital, it will create heat and it can warp panels. On Hoods, roof's and deck lids I prefer to use a chemical stripper. It's messy, it stinks and it may take several coats to remove the paint. After the first coat is applied let it sit the recommended time and remove what you can with a plastic putty knife and repeat until most of the paint and existing primer is removed. Clean your surface with lacquer thinner or similar product and remove the the left over paint or primer with your DA. I prefer a product I believe is made by Marhyde called "Air Craft Stripper". It's fast, it's efficient, it stinks and it's messy but it does work. When you are done stripping, don't be alarmed....you will find other areas on the car that require body work and or rust repair. Take your time, ask questions and make sure you don't take short cuts and you will have a much better finished product.
I hope this helps and if you need any more help, please ask.