Just to ensure I understand you correctly. You want to configure the iSCSI connection between the ESXi hosts and the storage using an independent iSCSI HBA in your host and in addition to this, you want to use in-guest iSCSI to access data on the same storage system?
That should basically work without issues. What you may want to do is to attach the VMs to a virtual machine port group with access to the iSCSI storage and configure the software initiator in the guest OS.
André