General visual studio aspx website questions

I'm trying to create a multi-directory aspx.net website using visual studio. I'd like the website to have several subdirectories so there will be multiple web.config files for different kinds of authorization.  I've been creating these subdirectories by making virtual drives with IIS, then creating a visual studio website in each virtual drive folder and adding the folders to my main website application.  However, I've run into some conflicts with the secondary websites and my main site (like having to remove most of the secondary web.config files' information).  I was wondering if visual studio offered an easier way for making aspx website subdirectories. I'm also somewhat confused about whether I need to delete the global.asax files or anything else within the subdirectories, and I'm not sure how I should publish the website when I'm done without potentially losing the pathway links between the aspx.net websites. Any help on how best to set up this web desig ...