I just apologized to you in another thread about this. In general, yes, the freemarker directory tree should be static. If we ever do change the location of files in the future, we'll make sure to have an upgrade task handle the location changes automatically so that you don't end up with broken themes.
Sorry for the double posting. I was just frustrated after working for several days getting my templates to work, and have (had) them checked into CVS. It's the price of an early adopter.
Thanks for your continued support and the 1.1 release. It's looking really nice.