You have not said what theme it is you have used, nor why you cannot set colors, fonts, headings and footers etc. in the shop add-in to resemble it? How close do you need the resemblance to be?
Off the top of my head, I would suggest retaining separate files for the shop, and possibly place them in a separate directory. This should allow you to setup the colors etc. for the shop without adverse impact on the existing site.
Alternatively, if you chose to put the shop files in the same directory as the existing site, you may need to rename the shop files if they clash. The idea is to make the shop resemble the site, whilst keeping them functionally separate.