How to pack your Mission
From The DarkMod Wiki
You should pack al your assets into a seperate directory following the same structure as can be seen in the various origina PK4 files. Then you can use any application to pack it into a zip file (Winzip, WinRAR, etc.). After it is packed you just rename the zip extension to pk4.
The result can be dropped either in the darkdod directory or in the base folder of your Doom 3 installation.