I use a modified version of the replacetext function to replace these keys with the right executables (e.g. I replace <bsp_compile_area> with "$INSTDIR\quake2\compilers\qbsp3.exe $8.map" which is all set ready for an ms-dos environment.
I also use a slightly modified replacetext function which allows me to use it like so:
Push "[Text to replace]"
Push "[Replace text with this]"