Leave the "id1" folder alone, with the same name and contents as always... you still need that stuff when playing a missionpack.
For missionpack 1, its contents should be in a folder named "hipnotic". Missionpack 2 should be in a folder named "rogue".
If you're going to play missionpack 1 then you should launch Quakespasm (or whatever Quake engine you are using) with the command-line argument "-hipnotic". Or if you want to play missionpack 2 then you should instead use the command-line argument "-rogue". (Along with whatever other command-line options you usually use.)
One more note, just to avoid confusion:
Missionpacks are a little different from other mods. Normally for a mod in a folder called "hipnotic" you'd use the command-line option "-game hipnotic" for example, to activate the mod in that folder. But the missionpacks are activated through their own special command-line options because they don't just activate a mod folder, they also change aspects of the engine code (dealing with weapons/items and the HUD).
Post edited January 03, 2016 by Johnny_Law