This is a compilation of some of my experience and techniques used during MGA body sill replacement. The short story is, new sheet metal was cleaned and sprayed with "zinc rich weld through primer" prior to spot welding.
The weld through primer comes in a wide variety of brand names. The common variety has finely powdered zinc as the pigment, as much as 50% by weight in liquid form, and maybe 80% zinc after the solvents dry off. It is electrically conductive to enable welding after priming. My personal experience says it works very well for spot welding, and acceptably well for plug welding with a MIG welder on new sheet metal. Some other people report having some problems with sputtering or blow through using a MIG welder. The last can on far right in the picture is copper based weld through primer, which some folks say may cause less problems for MIG welding.
I spot welded my body sill assemblies together before attaching them to the car body. I then taped over all of the weld joints and vent holes to seal it up (except for one large hole). I poured in Chassis Saver paint to mostly fill the box volume, taped over the last hole, and then rotated the assembly in all directions to coat the inside. Tape was then removed from one end to drain the excess paint into a bucket. After overnight drying time the rest of the tape was removed, and the outside of the assembly was cleaned with solvent prior to welding it to the main body shell.
After the new sill assembly was welded to the inner fenders, the outside was also painted with Chassis Saver prior to installing the outer rocker panels. Chassis Saver was also used to paint inside of the B-pillars before the outer closure plate was welded in place. For the A-pillars I used a swab on the end of a coat hanger wire to reach through inboard access holes to paint inside of the door posts. Let no nook or cranny go unpainted. The entire MGA body sill replacement process can be seen at www.mgaguru.com/mgtech/restore/restore1.htm