If you haven't been there before, you may not be sure sure of the general layout, i.e. the town of Siem Reap is the base for all visitors to the heritage area of Angkor Wat which includes ruined temples scattered across an area of maybe 10 x 15 km and is in driving or bike riding, not walking, distance from the town.
I was there for a week in October last year and I'm sure I missed quite a lot, but AFAIK there is only one functional Wat in the heritage area. It's not far from the main entrance of Angkor Wat, but outside the moat - off to the left as you face the causeway. It is modern, not very big, and not at all touristy.
There are lots of little shrines amongst the ruins, apparently set up by the people who work in the area, e.g. http://www.flickr.com/photos/50030099@N04/4605287285/in/set-72157623932840775/
. Look out for them - they bring some life into the place.
Siem Reap is quite a big place and is growing and modernising like crazy with all the tourist trade. I saw a number of temples but didn't have much time to visit because my whole focus was on the ruins. Bear in mind that Buddhist institutions, like everything else to do with education or culture, took a real hammering during the Khmer Rouge years and are still recovering.
Enjoy your trip!