I think you have the general "larger" understanding now.....
However, you CAN do what you want to do completely within Soho, with a totally custom look if you opt to get a custom Template made for you (
I had one made from scratch for under $75 from Ben at TemplateZapper.com), and for a few dollars more, I am sure they already have a solution-script in hand to deal with the sub-category issue!
I am however, still working on a suitable script to alter the shipping setup.
Having a totally custom look was
my main concern, and using the numbering scheme I outlined above was actually better "logistics" overall when managing my business and having associates understand it also......