Pak Explorer is superior -
place everything you have made in "maps", "gfx", "sprites", "sound" and "models" directories in the pak, as well as titiles.txt (goes in the root directory or the pak)
DON'T INCLUDE ORIGINAL HL CONTENT!! (the size will be too big)
that should clean up the ol' mod directory or map set a bit
btw,
Name you pak
pakX.pak
where X is a number from 0 to anything i think.
All pak files in a game directory like "valve" or "gearbox" must have a structure:
pak0.pak
pak1.pak - overrides pak0.pak but game references pak0.pak anyway
pak2.pak - overrides pak1.pak but game references pak1.pak anyway
and so on..
That's basically all you need to know about pak files...