This seems to be very common... home pages should outrank deeper pages, yes?. Are there any external backlinks (from relevant, authoritative sites) to your deep-content landing pages? Perhaps all your credibility resides on your home page. Have you done any off-page SEO for the landing pages?

If you have many inbound links or landing page traffic for the old page URLs, will you be redirecting those old URLs to your new URLs?

GA allows many sites per "Account" and many "Accounts" per Gmail login. So in GA, I created a few dozen Accounts and put up to 50 clients into each Account. Most clients have one or two websites, some have more, so I put the larger clients into separate Accounts (UA-nnnnn-xx where nnnnn is the Account and -xx is the website property.)

In Google Analytics I am monitoring over 500 sites for various clients.  ALL of that is under one Gmail login for admin, and you can assign access privileges to each web property uniquely, so each client can look over their results privately via their own Google login.