I think I have it narrowed down to the Eagle FishEasy 320C Color Fishfinder or the Hummingbird 565. So first of all which would you go with. Seond of all I dont really know anything about how to mount or run them. Do they run on regular household batteries or hook up to your marine battery? This is going on a 12 Pelican jon boat so mounting it is another queston. Dont really want to be drilling hole i my boat so what are the mounting options for the unit and also the transducer??

I would go with the Humminbird 565.  The higer pixel count, power and dual cone angles are all big pluses for fishfinders.  The color is nice though.  They will run off of your marine battery.   If you are looking at mounting it try one of these

http://www.cabelas.com/cabelas/en/templates/pod/horizontal-pod.jsp?_DARGS=/cabelas/en/common/catalog/pod-link.jsp_A&_DAV=MainCatcat21276-cat21402&rid=&indexId=cat21402&navAction=push&masterpathid=&navCount=1&parentType=index&parentId=cat21402&id=0000844

It will allow you to mount it on your boat without having to make any holes.  You can put the transducer on the bottom of the trolling motor as well and mount the head unit somewhere on the boat.

I have the 565 and I like it. I have some power problems but I believe that is because I have a lot of "stuff" attached to one battery. Overall, it's great though--reliable.