host agent utility / boot from san / windows cluster

Do you install the EMC host agent utility on a windows server that is boot from san.  It's also a windows cluster.  I've set the cluster up successfully by just registering the initiators manually in unisphere.  If I go back through and install it I'm wondering if it will jack up what I've done.  I have 4 hba's in each one of the servers in the cluster.  2 hba's go to a storage group just for the boot lun and 2 hba's go to a storage group that is for the clustered disks.  It's my understanding that if I used the host agent utility to register the initiators with unisphere all the initiators from a single machine would be under one host which I didn't want.  Thanks for the help.