.net installer and setting up file extensions

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.NET

installer

I am a complete newb to installers, but so far I have made decent progress. I am stuck on one aspect that I can't quite sort out. My installed application has a few files that the executable works with in order to function. I have successfully created shortcuts in places like the desktop and start menu as part of my installer. However I can't get the same type of behavior to work when I add a file type. So if I add the file type, and then set the command to be the primary output found in the application folder, then I would have hoped that would work. However, once I install, I can tell by some error logs I have in my app that it is looking for files relative to the file with the extension I just clicked on, not relative to the application folder. So rather than looking for c:\Programs(x86)\MyCompany\MyApp\Settings.xml it looks for Settings.xml in c:\MyFileFolder\Settings.xml because the file that I clicked was in c:\MyFileFolder.

That obviously causes actions that depend on that file to fail. I can't figure out what I am doing wrong on this. Does anyone know what I am missing? I have followed the steps on some MSDN walkthroughs but they don't say anything that would warn me about this issue. I tried seeing if I could browse to a shortcut that I have created for the installation, but that wasn't working.