A CMS is a content management system, essentially it is a system written in some programming language that makes it so the client can edit their site. Usually the get set up for larger projects because most companies charge a lot for them.
About the layout, I like the three butotns on the bottom and the links that are just above them. I would suggest though that you try to put some more content into the large box above them. It is in a prime place for viewers to see and you could transfer a lot of information there. Try looking for some images, and possibly putting information such as phone numbers and address there, so they are very easy to access.
Popup boxes would be very easy to do with a little bit of javascript. You may want to even try out something like a version of lightBox (
http://particletree.com/features/lightbox-gone-wild/) or check this link for demos (
http://particletree.com/examples/lightbox/). It provides a nice style and also is not interrupted by outside software (popup-blockers).
Also if you like the lightbox type thing, I have a smaller version I wrote that can be used. I have not used the actual lightbox code (posted above), so I am not sure if it is difficult to setup.