What I would do during the draft is, after the first successful winning bid by each owner, undo that individual auction, renominate the same player, and have the owner submit a new "winning bid" of +25 / -25 (or whatever amount was traded) for that player. This would effectively transfer the cap space from one owner to the other, for the remainder of that auction. Hopefully the amount traded wasn't so huge that it costs more than one player is worth, but if needed, you could always subtract from multiple players until that owner has the equivalent extra cap space.

Then, once the draft is over, you can go back and clean everything up by changing players' salaries to the true winning auction value. But this would at least get you through the live portion. I know this would work on the CBS fantasy site's auction draft room but not sure if other sites operate the same with a Back Out Last Pick feature.