Back up your skin1 directory and put it somewhere safe.
Then start tackling the changes you want to make. I started with a basic concept in my HTML editor, then translated it over template by template. [Which is really not much fun...]
The style sheet controls LOTS of things, so you might want to start there first, then make adjustments.
The other thing that saved my sanity for the first few x-Cart edits was adding a < !-- template path/name -- > to the beginning and ending of each template, one said begins, one said end.
I *wish* that were an option to turn on and off -- the debug panel and the webmaster mode only go SO far.
deb