Well,
I just tried a web project , targeting 10.1 just like you (going through the new project wizard)
I imported all modules and sources as I thought I would.
Here's my setup and compiling works :

Now I don't actually know how to set things up properly, maybe this is wrong,
on the left you see src/src libs (added via project structure >modules), I had to right click on them and Mark Directory as src so I might have done something wrong in the first place here.
I suppose you know better how to set that up.
Anyway, autocomplete works when I mention something from citrus and I also am able to import signals from the signal.swc so I assume I included them correctly.
I'm using CitrusEngine, not StarlingCitrusEngine because you said you would be using the flash display list only.
the compiling and swf runs without errors...
Should I check something else ?