OH man. So many hours in Quake - I'll have to learn how to get one of these engines up and running.
1) Download and unpack ironwail (best engine).
2) Copy id1/ (from your official Quake install directory) to your ironwail directory
3) Launch ironwail
Adding and launching a mod:
1) Unpack the mod into your ironwail directory
2) Launch ironwail
3) select the add-on
If you have quake on steam, ironwail will automatically detect it.
If you want to directly launch into a mod you can create a shortcut or use command-line parameters.