I've just started using wordpress and I found out about Atahualpa theme shortly after. The problem is that I need to run a mult-site rig and after happily deciding on multiblog I noticed that Atahualpa is dependent on file structure at least for the header images and logo. Is it possible to let the user decide the location where the theme will look for files. Meaning, if the theme would store the location values in the database then it would be completely usable in multiple-blog enviornments.

Are you using WPMU? There, each user should be able to have his own images/logo