idStudio tends to lock up when switching to the engine tab. The best way to work around this is to have a tab that doesn't use the GPU (such as console) near it, switch to that tab, then to engine.

The mod portal and idStudio are both running under separate steam apps and therefore different prefixes. First off, in your mod portal settings, change the paths away from the defaults on C: and into something both apps will see, and whatever you make in idStudio should now show up in the mod portal. Because of the separate WINE prefixes, idStudio cannot communicate with the mod portal; inconvenient but not feature breaking, just click on "test mod" and idStudio will copy your packaged mod over to the active mods folder you set earlier by the time you see the error message telling you the mod portal needs to be running. You can also find an option to publish a mod in the Portal itself, so don't worry about the upload mod button in idStudio not working.

Note: I only recently discovered that Steam has an environment variable to set a compatdata path, but using what I learned above I played I was fine without it.