How to protect two BIW parts from rust.

I used to design hemmer machines. We used a non-welding solution that used an epoxy method. That is, we had a marriage machine that accepted the outer skin first, then a robot applied an epoxy around the flange of the outer skin. The inner skin of the panel was then set into the marriage machine which centers it on the outer skin. The married panels where then either lifted by robot into the hemming machine or moved into the hemming machine with a conveyor. The hemming machine then "bent" the outer and inner flanges at the same time so that a "hem" was formed. NO WELDING, NO WATER permeats the "hem" because it is a continuous seal from the epoxy thus, NO RUST.

I assume you are spot welding panels on cars etc as you asked in the Automotive section.

Using zinc rich spray on the surfaces before welding can give some protection from corrosion .It is important to have intimate contact between the two surfaces to ensure the weld takes place at the tip points. Also if using single contact welding it is necessary to dimple the spot point with a back up block if you can get access , then fit ground clamps on either side of the weld preferably on the far side of the place where the spot will be done, this is important.

Some experimentation should be done on scrap to arrive at the best setting which can be fussy due to the paint.

Google Rust Bullet.Good stuff.May be what you need.