Does iControlWP Support The Management of WordPress Multisite Websites?
It can be network activated. However, there is currently no support for sub-sites of a WordPress WPMS site.
So, yes, you can connect WPMS sites, but there are no controls for the subsites. We've found that this to-date hasn't been a requirement for most admins. You're essentially network activating plugins when you do so via iControlWP.
Worpdrive works as normal - again, there's no sub-site backup/restore etc.
Note: If you see anything strange with the behaviour for WPMS sites, please let us know and we'll take a look.