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I would like to know how to run multiple DNS Seeds on the same node.

It seems fairly straight-forward as described in: https://github.com/sipa/bitcoin-seeder

For example, I want two DNS Seeds: bitcoin-seed.mydomain.com testnet-seed.mydomain.com

It seems as per the existing instructions I would either need to run multiple VMs or at the very least create new users and redirect port 53 to them. (I am not sure I can redirect port 53 to multiple users)

Is there any way that I can set this up on one VPS with Root access?

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Asking this question on Super User might have resulted in a quicker and more response as this is strictly speaking not limited to Bitcoin.

Sipa's bitcoin-seeder allows you to run the DNS node on a port other than 53, so that you could set up a DNS seed for each of the networks you want to support. In order to receive incoming queries and respond to them you'd then set up a BIND server that acts as a slave for the individual subdomains and then delegate incoming queries to the corresponding bitcoin-seeder. The zone configuration of the BIND daemon does allow you to specify ports other than port 53.

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