My advice, and what I've done:
First, take a look at all of the various implementations linked in the Reviewer's Corner. Get your own idea of what looks good, before you get wrapped up in the difficulty of making it possible.
Then, install ZC. I installed without the demo products.
First, go through every FAQ category and browse the titles. When you see a title for an article that you're interested in implementing, open it into a new tab(or window). Follow the instructions therein and then close the window. After you've completed this process once, you may be more ambitious, so go through the FAQ titles again. Repeat until you're satisfied that there's nothing more in the FAQ that you want to implement.
Second, take an honest look at your site. Ask yourself, "What could this use?" "How could I make this look better?" "How could I make this more usable for my visitors?" Make a discrete list of changes that you'd like to make. Work on one at a time by searching the forum for a two or three word phrase that describes the problem. You might have to wade through four or five pages of topics to find two or three posts which help, but 95% of the time you will find the answer. To find the right post, I usually go through every page of results that the search returns, opening into a new tab any topic that looks like it might relate to my problem. Sometimes, you might not find the answer but will find better terms to search for.
If you have some programming experience, once you've found every solution that's described in the forum, you might be able to go about making your own simple solutions. Like Mary says, use the over-ride system to make reversion a snap.
At some point, I think it's a great idea to start all over again with a fresh install. You'll be in a position to create a much better site with a clearer idea of what you want and a firmer grasp on proper practices.
Of course, there's a whole other side to designing your site which I'm unfortunately unqualified to address. That's the artistic side. Luckily I have a wife who's gifted there.
After all of this is completed there's the marketing side. I feel that there's disproportionately little conversation on this issue, but there is plently of information out there which you must absorb in order to have a successful business.
Best of luck,
Joe
Now J_Schilz
Integrated Checkout Without Account (wiki w/pics, demo, download)