activate vs network activate issue


I need some help here with plugin activation on main / site vs network activation. Here's the scenario. I set-up a wordpress install and put a set of plugins on it, inlcuding buddypress set, then used enable multi-site plugin to set-up the blogs. I then finished off installing some other plugins into the plugins directory - using add new plugins on the dashboard - and installing zip files from my desktop.

I then realised that I could not activate these only on my / site, as they don't appear in the list there. I had assumed that this top level site would have access to all the plugins - which I don't want on the user network - e.g. buddypress, membership etc.

So, realising my mistake, I took enable multi site out and put my wp-config back to single, and then the full set of plugins were there on my main site. I enabled what I needed for that site then re-installed multi site, only to find that my main site plugins reverted to the original subset.

So, this must be cached or stored somewhere and I need to be able to add to this without the multi-site enable changing it back again and putting me back to sqaure one.

In general, this process of activating plugins seems a bit problematic. A lot of the multi site ones downloaded from WPMU only work when multisite is enabled and had to be stripped out of the plugins folder again as they took the site down if activated before multi site was enabled. So a guide on how and what to activate at main site level, and then what to activate across the network would be good - e.g. some of the global post plugins kill the main site in this way.

As I understand it now, activate works at main site level, network activate puts plugins on all user sites and putting plugins in mu-plugins ensures they can not be deactivated by users, but this issue of how to configure the main site is still there, and surely it should take precedence and sit above the others somehow. Or am I misssing something.

Your help to figure this out would be appreciated. I want all my plugins to be available at root/main site level and work from there, hopefully without having to reinstall the whole wordpress install.