Welcome to the VMware Communities forums. It's no problem having ESXi on 3 seperate networks.
The default install of ESXi will create a virtual switch (vSwitch0) with a management port and the Virtual Machine port group.
You'll want to create another 2 vSwitches with the other 2 NICs. On the Configuration > Networking tab click Add Networking. In the Add Network Wizard you'll select Virtual Machine as the Connection Type and on the next screen you'll be able to create a new vSwitch with one of the free NIC ports. You can then repeat that process for the other NIC.
When you configure your VMs, you'll select a Network Label that is appropriate for the physical network you'll want to connect to.
Depending on your networking requirements you could configure things differently. If you're using vLANs then you can have a single vSwitch with multiple virtual machine port groups (each tied to a specicifc VLAN).