i want to install server 2012 on a new machine which will run side by side with my windows small business server 2003. When i install it however i get the choice of clean install or migration. I do not want to migrate i just want to run it side-by-side as the server 2012 machine will be used for SVN. My confusion is when the clean install prompt comes up for what i want to call the internal domain name, i cannot let it join the existing domain name. If i give it a new domain name will it simply run side by side on the server or is it going to ruin all my existing network setup.
You can't have two SBS/Essentials servers on the same domain. This is a published and documented limitation of the product. There is a 7 day migration period that can be extended twice. The longest that they can co-exist is 21 days for migration, after that, a built-in mechanism causes them to start rebooting.
You're going to need a full server OS.