Qtopia (and Opie II !!) do not require you to build in the source tree. You can "shadow build' using a different directory for compiling, keeping separate your work sources and your build tree. This keeps things nice and clean, and is easier to maintain and work with. It also makes it possible to have builds for multiple devices using only one source tree.
Only thing you need to do is set QTOPIA_DEPOT_PATH to where ever your sources are.