Directory mapping and merging in git

I have an online store running OScommerce and I use git to manage my development the Official release also uses git.

I currently go through the changelog and read each change to each file, type said change, and commit. As you can imagine this takes forever and increases the chance of me typing and commiting something wrong.

I'd like an easier way to manage updates/merging from the official git repo without having to hand edit each file and commit. I know git has the merge command but I run into two obstacles when thinking about this problem.

1. The file structure isn't the same.

   All my files are located in shop/ and the default is catalog/

2. I just want to merge changed files in my shop/catalog folder not download everything else.

   I would rather not download/redownload every readme, changelog, and other removed files every time I get updates from the official repo

How can I update/merge files without retyping every change in manually taking into account the above two problems? What's a proper workflow for this situation?