so sm1 at least I got working by installing the secret missions pack into the pcgamer folder then re-extracting the pcgamer folder over that. sm2 didnt work at all though (black screen)
what makes that a bit more bizarre is that the same number of files are present in both that folder and my kilrathi saga install folder yet the sm2 in the ksaga folder works fine (using the ksaga wc1 exe) while the sm2 in the pcgamer folder doesnt so presumably the difference is in the wc1 exe file that is cracked!
so what i'd suggest is that you make sure you dont restore the cracked wc1.exe after installing the secret missions or neither wc1 or sm1 will work - sm2 may never work.
IGNORE THE ABOVE! I'M ONLY LEAVING IT FOR POSTERITY!
RECIPE TO GET SECRET MISSIONS WORKING WITH PCGAMER KILRATHI SAGA
extract the pcgamer wc1
copy all the files from the wckssm12.zip (the kilrathi saga secret missions 1 and 2 zip file) to the wc1\gamedat folder overwriting where necessary (briefing.002, camp.002, commsm2.dat, install.dat, intro1.dat, midgame.v06, midgame.v07,midgame.v02, module.002,pcship.v05, planets1.vga, series.vga, ship.v19, shiptype.v14, talking1.vga, title1.vga, wingmen1.vga) EXCEPT:
sm1.exe, sm2.exe, transfer.exe wc1.exe wing1.exe, sm12inst.exe
now copy sm1.exe, sm2.exe transfer.exe into the wc1 folder
that should make the games work ok!