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

For the DNS seeder to properly listen and respond to incoming DNS queries, it absolutely must be listening on the standard DNS port # which is 53. You can normally only have one port open per computer/ip, so running two DNS servers on the same VPS is either very difficult or impossible.

I believe the simplest way to run two DNS seeder apps on the same VPS is to setup the 1st using the original local DNS server mode and the 2nd using Cloudflare API mode.

Take a look at the generic-seeder app, which is a clone of the original bitcoin-seeder that makes it easy to configure for a new coin and also adds additional features such as Cloudflare mode: https://github.com/team-exor/generic-seeder

There's even a full setup guide that explains how to set up and take advantage of Cloudflare mode: https://github.com/team-exor/generic-seeder/blob/master/SETUP.md

Full disclosure: I am the author of the generic-seeder.

Update: dbkeys released a multi-seeder earlier this year based on the generic-seeder source. It runs a single seeder app that is able to respond to up to 10 different networks simultaneously: https://github.com/dbkeys/multiseeder

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