Question
I don't want to use sub-domains, but would rather the set up be www.domain.com/1, www.domain.com/2 etc. I can do this with new wp installations for each - but I go through the home wp site, create a page name 1, then go to Cpanel and create the 1 folder with new setup of WP - this all works, but is this proper?
Answer
What do you mean with large? WordPress MU is handy when you want to centralise plugins and themes. If your sites vary in that way I should propose to use single WordPress installations and control its throughout the Cpanel.