ps:
Now I found, that using either pak programs is not necessary, you can just copy files into folder http://forums.inside3d.com/viewtopic.php?t=3196 . Which solves my problem - I wanted to automatically compile and update progs.dat.
if I'm reading this right, its:
qcc -pak mygamedir pak0.pak
qcc -pak2 mygamedir pak1.pak
run it twice and you get two pak files.
of course, that requires that your precache_model and precache_model2 calls are not confused.
oh, and this feature is of more use to people that actually want to build the entire thing from scratch, what with the fact that you probably don't want to change all the precache_sound/file/model calls to choose which files are actually compiled...
blurgh, lazy.
alternatively you could feed it some dummy qc file with a lot of precache_file/precache_file2 calls.