Oh, I see - I think you are asking if it is possible to change the contents of a resource file in a form template programatically?
You can access the file, but I don't think you'll be able to save the changes - you'd have to save the template as source files, and update the file, then repack it up.
It sounds like your current approach of accessing the files from their network location may be the correct way to go here.
To open a resource file that is part of your template (MSDN link):
this.Template.OpenFileFromPackage("FileName.txt");