I suppose it depends on how you configure your network. If you, indeed, have 2 separate vlans, one for iscsi traffic and one for CIFS, then you have 2 choices:
1. The simplest is to just have 1 interface on each vlan. The traffic will automatically separate assuming the iscsi and cifs hosts are accessing the storage on the same local vlan/subnet.
2. You can vif the 2 interfaces together, and then impelement vlan tagging on your switch and controllers. On the storage side, this will create 2 interfaces vif-## where ## is your vlan #. Then each interface is configured separately in ONTAP. Of course you must configure your switch to do this as well. This doesn't separate your traffic on the individual interfaces, per se, but potentially gives your a larger or more redudnant pipe for both protocols.
If you only have 1 subnet/Vlan, then it's tougher to make sure the traffic stays totally separate, but your best attempt will be to assign differnet IPs to each interfaces and then have the clients access the controller by the proper IP. This can be done via DNS names, etc.