Intellij takes care of calling the compiler with mxmlx/compc... and u can't override that.
According to this old post, modules dependencies benefit from incremental compilation when no changes are detected ...
@marpies made a detailed guide in his blog. Is not the same, but helps a lot I think.
Although more tedious, you could create a special run configuration to run a batch file that takes care of everytihng, but I'm afraid u will have to setup everything by hand ... or use ant, gradle, etc..
I only tried @marpies suggestion to be honest and works fine, the FCSH approach works fine with the included tests, but for a real project, requires tons of setup I'm afraid.