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I have a managed switch. I’m a little confused how everything would be hooked up if I’m using a vm for pfsense and another vm for some Linux distro. I want the router and that distro to be isolated from my other vlans. Could I use the onboard nic hooked up to the switch to put the distro on its own vlan?
You can absolutely attach each VM and even the host to separate NICs which each connect back to the switch and has its own VLAN. You can also attach everything to one NIC and just use a virtual bridge(s) on the host to connect everything. Or any combination therein. You have complete freedom on how you want to do it to suit your needs. How this is done depends on what you're using on the host for a hypervisor though, so I can't give you exact directions.
One thing I should have thought of before; if two NICs are on one single PCI card, you probably can't pass them through to the VM independent of one another. So that would limit you to doing virtual networking if you want to split them.