I get a message at the top left of the screen saying "Can't find maps (map names)". Anyone know what I need to do?

You need the file pak1.pak from your original Quake CD and put it in /quake/id1/ folder.

I'd guess you downloaded the nQuake package which is great for multiplayer, however it only contains the Shareware version of Quake (i.e. only first episode) due to licensing reasons.

Welcome to the QuakeWorld.nu forum btw.