I have not gotten those cap/rotor kits so i havent had to deal with the problem, but i would think that as long as u kept the firing order the same and made sure the rotor was at the #1 plug when #1piston was at TDC, it should be good to go.
I know a couple guys run those caps on here, maybe they will chime in. Or couldnt u just use those "tabs" on it to compare it to your old cap, and find which post would be #1 if it were to be marked?