So when I go to make a 1U rack, the rack is really thin, and the modules overlap by quite a lot. Is there a setting to get it to visually appear to scale?

Go to Rack edit and uncheck the checkbox for 1U Tiles.
Normal Eurorack modules are 3U heigh. 1U does not mean one row. It is the size of the small utility modules that are available.

Ah, that makes sense. Thanks!