Pretty sure the Avid MediaFiles folder, where all your footage and pre computes are stored needs to be at the root level of a volume. so the best you can do is to keep your project on the same volume. If you don’t want the footage mixed with other projects in the same MediaFiles folder, When you start a new project, you can increment the number of your footage folder up to a higher number(Avid MediaFiles/MXF/1) and MC will start a new one at number 1. This will keep everything separate. You have to be real careful with this, if you bounce between projects, but it can work.
The question is why do you want to bypass the Media Tool..which is designed to deal with all this and is better suited to deal with the way Avid manages files. It’s a bit like wanting to repair your car and refusing to use a screwdriver.
Avid is not FCP7. The reason media management is more solid in Avid than other NLEs, is its database and file system. It’s rigid, but its very reliable. If you try to go your own way, you are asking for chaos.
(This applies to “traditional” Avid managed media. AMA media can be managed more like FCP, but not surprisingly, it’s more temperamental. I avoid editing with AMA…just use it for selects, then transcode to Avid media)