I have a server that has two networks on it, one to production and the other to an iSCSI network.  If I backup that server and the iSCSI drives are seen as local will ShadowProtect support this configuration?

You can backup logical volumes on any iSCSI LUN which is seen as a local disk on the machine on which the ShadowProtect agent (the ShadowProtectSvc.exe NT service) is installed.