I had issues getting to grips with CompilePal for packing (even though I use it for compiling) so I still use VIDE.
Open up the Pakfile Lump Editor (
this button) and open up your map BSP.
Click scan. You'll want to scan /Team Fortress 2/tf/ first (wherever you have that located, it's usually in C:\Program Files\Steam\SteamApps\Common\). Hit Scan again.
You'll see a list of a bunch of stuff, if you click Auto on the right under File Options, then Apply slightly to the left it'll add everything there to the pack.
For any custom folders, repeat the above bit but instead of /Team Fortress 2/tf/ do /Team Fortress 2/tf/custom/[name of folder]/.
Once you're done packing everything, hit Save on the main bit and you're done. Note this packs all skyboxes, materials, overlays, models etc. but won't pack anything not in the hammer level "physically" like sounds or detail sprites. (I use Pakrat for those still)