The only difference between creating the LUNs from the filer versus SnapDrive is the way the initiator groups are created. SnapDrive will automatically create the igroups on the filer and map the FC initiator(s) of the host. If SnapDrive already detects and snaps the LUNs I think you are good to go. A good test would be growing/shrinking a LUN from within SnapDrive. If you want to use the automatic igroup just disconnect all the LUNs (assuming there's no data on them yet), delete the manually created igroups, and reconnect the LUNs from SnapDrive.
I'm not sure I understand your question for part 2. The LUNs need to be present on the host (SnapDrive is a prerequisite) when installing Snapmanager. Run the configuration to move the log and data files, etc., to the SAN and you're good to go.