You should review the source code and consider the WebStore set of projects as an example of how to layout your own projects. .csproj files just tell VS which files to compile it has no bearing at runtime. At runtime all the matters is that your dlls are in the bin folder under the Web project and that your .ascx and .aspx files if any are also copied somewhere in a folder of the web project. You should use a post build event to copy the files and look at the post build of WebStore for an example.
The path to the .ascx file that is the starting point of your feature is the only thing mojoPortal knows about at all, and that comes from the feature definition file (see the link Jamie posted) if using one or else it is whatever you put in manually for the path to your control using the Administration > Advanced Tools > Feature Installation UI pages. Using the feature definition file just automates populating the info, the setup page process it for you. Again as far as configuration that path to your user control is the only thing mojoPortal knows about your feature, other than that the dlls must be in the bin of the web project and you make sure your internal links use SiteRoot + /yourpath/... based on wherever you decide to put your files (using the post build event)
If you feature has supporting pages then you would link to them from your .ascx so any links are internal to your feature, and like existing features the pageid of the cms page and the moduleid of your feature instance you would pass also in the url to your supporting pages so that you can use mojoBasePage methods to enforce role based security, again study the code for existing features for examples
Hope that helps,