I'm running WPMU 2.6.3 with Multisite Manager and Plugin Commander. Reading your first post several times, I'm still not sure exactly what you're asking.
Anyway, in my experience, you shouldn't be trying to use both the top level Plugins menu and Plugin Commander. Choose which one you're going to use and stick with it. Plugin Commander should reside in the MU Plugins folder.
With the set up your describing, you need to hide the top level Plugins menu. Do this by logging in as Admin to your first site and go to Site Admin > Options and scroll right down to the bottom of that window, to the 'Menu' section. Untick the 'Plugins' tickbox. This will then hide the top level Plugins menu across the whole of that site (including subdomains).
Repeat this across each of your sites (so 7 times in total).
Site Administrators then manage all plugins via Site Admin > Plugin Commander (enabling for user activation, mass deactivation etc). Users activate and deactivate what the Site Admin has allowed plugins via Manage > Plugins tab.
Simple as that, although I do find Plugin Commander a little buggy for doing Mass Activation etc.