Header and post features

It would be great of the “Header Image and Color” feature allowed us to enter a header logo file, and the position of a post could be assigned by number. I am using 2.0.5 and I’m geting a headache trying to figure out how to replace the default theme template header with my own header file and it just shouldn’t be that hard to do. I realize there are several files where it can be done but none of them seem to work properly.

Thanks for your help.