In terms of customizing subsites (and other packages) I discovered a way that answers my question:
If I create a subsite called students and mount two apps forum and news. To have a nice homepage for the subsite I simply create a directory /SERVER/www/students and in there write my fancy homepage in index.html (or .tcl/.adp) .
The request processor will give precedence to /SERVER/www/students/index over /SERVER/packages/acs-subsite/www/index.tcl for the url http://mydomain/students
Any apps mounted like students/forum or student/news will still be accessible from links in my fancy homepage.
