You can have all three vlans trunked on both links, created a portgroup for each vlan and set the vlan on the portgroup. Communication between the vlans will be handled a router or the switch itself if it is capable of routing. Use both nics as uplinks and the default teaming policy Route based on the originating port ID is sufficient for this configuration.
How are presenting storage? Over the same two nics...iscsi / nfs??