After reading about notepad2 from some other bloggers in the community (Omar), I downloaded it and have been using it for a couple weeks. If you desire more from notepad I would highly suggest you take a look at it. I took Omar's advise and just replaced the existing notepad with it and I haven't had any problems. The only thing that bothers me is that it resuses the window by default. So you can't open more than one file by clicking on the files themselves you would have to do it through notepad2, by the open new window option.
Well it finally bothered me enough to try and figure out how to fix it. I looked through the documentation and it said something about disabling reusable-windows by using the "\n" command line option. I thought there had to be a registry setting or something so I opened the source code and sure enough there is a registry setting.
Disclaimer: Modifying the registry can cause serious problems that may require you to reinstall your operating system. I cannot guarantee that problems resulting from modifications to the registry can be solved. Use the information provided at your own risk.
Under [HKEY_CURRENT_USER\Software\Notepad2\Settings] you can add a new DWORD value with the name "ReuseWindow" and give it a value of 0. This will have it open a new window by default.
I figured I would share this just in case anyone else is in the same situation.