You can use mission packs by moving them to the "id1" folder.
Quit Quake.
Rename the file "PAK0.PAK" within the mission pack folder to "PAK2.PAK".
Move the file "PAK2.PAK" from the folder of the mission pack to the "id1" folder.
Start Quake.
Using mission packs by dragging them onto the Quake application icon
Using mission packs from the startup dialog
Using mission packs with AppleScript
Using mission packs from the command line