Your X-cart bible:
http://forum.x-cart.com/showthread.php?t=21529
I use Dreamweaver CS3 for all my editing and CuteFTP 8 Pro for all my file uploading. I had a basic understanding of html coding when I bought X-cart. It took me a month before I was able to go live with my site (just last week). It takes some time to get used to what you are looking for.
In a nut shell, like I explained to my mom lol, X-cart to basically like a big closet (customer/home.tpl) with lots and lots of shoe boxes inside (templates). Every file is called upon using smarty tags. Weather its a language file (which are edited in admin area) or php files (which are the programming files) or template files (.tpl files, your design files). Changing colors would be in the CSS (skin1.css). When you want to edit something you have to find that specific template that is being called upon. Like the logo your talking about. If you look at customer/home.tpl you'll notice that it calls upon head.tpl inside head.tpl is the logo you'r talking about. You can either change the logo name in head.tpl to your own name and reference it in the images dir or you can overwrite the xcart logo in the images directory.
See the link above for what templates contain what.
BTW, search box on this forums has helped me tremendously. Take some time and LEARN what you are doing and you'll be like me, after a week you'll post a question only to answer it yourself and going back to delete the post because you figured it out while waiting for an answer.
The best advice that I could give is take your time and don't get frustrated. I've only been an x-cart member for 5 weeks and I'd recommend it to anyone. Very easy to do things once you understand the concept.
Oh... read the manual too, helped me alot.