Installing a source port is incredibly easy, and doesn't require much installation or setup. Simply put: drop the source port into the folder where your id1 directory resides and run it. On startup, the source port will look for that folder, along with the PAK0.pak and PAK1.pak files inside id1. If it can find those, the game will start up. The source port and the original game executable can exist in the same folder, as long as id1 is visible to both of them.
If you just freshly installed Quake on Steam, I would highly recommend also grabbing the soundtrack pack here - for some reason the Steam release doesn't include the game's excellent (and mostly ambient) soundtrack from Nine Inch Nails's Trent Reznor. 2b1af7f3a8