Sure u can. I do it all day long here @ work, but i also use the standalone gcc-compiler, when using precompiled libraries, like xml2 and such.
StormC4 works absolutely great on WinUAE.
The debugger is really useful, just print out the *.pdf document and read yourself through it first.
The only "problem" with stormC is that it's developed by Haage & Partner .. .
:-D