For the -current- version of mono i think you should install the deb file i made for compilers here :
http://wardenclyffetower.com/MaemoFi...-1.9.0.all.deb

This wont be necessary when 1.9 is officially released because they are making repo packages for compilers themselves

With that installed you dont need mcs directory, set up your own source directory or directory tree without compilers in it.

Then you can copy your source files to any directory you want and compile like :
mcs hello.cs -pkg:gtk-sharp-2.0

Your source code files should be owned by user (or user should have write permission to them) so if user doesnt have permission, then sudo gainroot and run emelfm2 (as root from xterm) find the file, highlight it, hit menu key for context menu, choose actions submenu, change permissions, and click the 'write' checkbox for all three user groups... then exit emelfm2 and exit xterm