One of those little known things (and hence sadly most underused IMHO) about Virtual PC 2004 is the ability to redirect the location of where virtual machines are created by default. This is done through the "MYVIRTUALMACHINES" environment variable.

If you're looking for documentation on this, it's in the readme file for Virtual PC 2004 SP1 which is available online here or in readmesp1.htm in the \Program Files\Microsoft Virtual PC\Documentation\<language>\ directory.