Hi G,
I use Netapp VSC in Vcenter and dont have any issues with it, its a very powerful tool to have! I am still on 4.0 as i havent got round to upgrading yet but can give you some general things to check.
Did you register the VSC with VC after installing it? If not, enter this url on the machine where you installed VSC - https://localhost:8143/Register.html, then you can register it to your VC server.
For adding controllers etc I always do this from the VC GUI Home>Solutions and Applcations>Netapp
Then within the VSC console under Monitoring and Host Configuration>Overview you can add the controllers. Above you said "I can Putty into the SP's no problem" - As you are using 3240's these have a specific SP port for out-of-band management, I just want to check that you are not trying to use the SP ports for the VSC, you should use e0m or any standard interface.
Regarding your ESXi host being non-compliant, this is for Netapp/VMware integration best practices. Adapter Settings, MPIO Settings and NFS settings are checked against these best practices. You can remedy them by right-clicking the entity and selecting "Set Recomemded Values". It changes things like queue depths, HBA timeout values (eg I beleive the time out values are too short by default and need to be increased slightly to allow a Netapp cluster failover to complete so ESXi doesnt flip out), MPIO policy changes to Path Selection to RR if you are using ALUA on the Netapp (which you most definately should be if you have FC Datastores)
I hope you get this working OK,
Gav