How are your wads and source ports set up? (folders)

[Deleted_Account]

They're all lumped into one folder.

[Stupid Bunny]

All the PWADs are in C:\Games\Doom, within which there are separate subfolders for each sourceport, a subfolder for modding utilities, a subfolder for various resources and a subfolder for IWADs. I also put jokewads in a separate subfolder, and I'm not sure why. Anyway I just click and drag the PWAD(s) I want to play over the sourceport's shortcut and play that way, which works okay for me generally. For whatever reason I store Vanilla Doom separately in their respective subfolders in C:\Games\DOS\. I think the extracted SKYMAYBE is in there too.