First I'd try to just create a regular .zip and rename it to ..pk3...
If that doesn't work you can try the following:
(not sure if this will work, but worth a shot)
Find a .pk3 in your SOF2 dir, and copy it with a new name (ie "my.pk3).
Open it with WinZip, WinRAR or similar program and delete all the files in the .pk3.
Add the files/directories you want in it.
Close file.
Now SOF2 should hopefully be able to use it.