WOW! This is my territory! LOL! There are quite a few factors that will determine where to stay etc..
1. The CAT arrives in Yarmouth. I'm assuming you mean you're getting the CAT (the high speed ferry) from Maine (I haven't heard of 1 into Halifax, but I may be wrong). There are usually 2 ferries a day. If you arrive in the evening (I think it gets in around 7:30 our time (6:30 yours) you'll have to decide how far you want to travel. Are you bringing your own vehicle? Probably MUCH cheaper than renting.. even paying the extra for the ferry.
2. Halifax (capital city of Nova Scotia) is really the HUB of the province, in my opinion. It is approx. 3 1/2 - 4 hours away from Yarmouth.
3. There are LOTS of places to stay.. bed and breakfasts, hotels, camping etc..
4. How much time do you plan on spending? Yarmouth is actually on the southern tip of the province, you could always do a "loop" and take 1 route to Halifax, and another back to Yarmouth.
5. What you want to see depends on your interests. There is Peggy's Cove, there are beaches EVERYWHERE!, lots of historic sites, some great museums, casino, golf, hiking trails etc.... you name it!
6. WEBSITES:
<a href="http://explore.gov.ns.ca">Explore Nova Scotia</a>
<a href="http://www.yarmouth.org/">Yarmouth County Tourism</a>
<a href="http://www.halifaxinfo.com/">Halifax Regional Municipality Visitor Information</a>
Sorry this was so long!

Ask away if there's ANYTHING at all I can help you with!