I do it all manually. First I make a zip file with winzip. Then I move all the folders into it. Then I rename it --the file extension-- to .pk3.
If packscape can do it though, then new mappers should just use it. Many times we see people who use a texture that is not included in the .pk3 (and wonder why they have red-white-blue in the place of), or they name the "maps" folder "map" and wonder why the game can't find their .bsp file. Some people have named shaders the same as an important game asset, then when they fire up their game their client hud is showing different colors or some other off-the-wall thing. All of these things happen to new map makers --they all happened to me. Let me not forget the issue with models that are not properly packed....