I have setup AirPrint via CUPS in Ubuntu 12.04.03. This works through my main router, when my iPad and iPod are on this wifi router. That router is the main ADSL into the house. I then have another router, a MikroTik Routerboard, on an Ethernet cable attached to this. I use both of these networks for different iDevices, however the CUPS server is attached to the main router.

I think AirPrint only works on the local router, but I need to use it on both networks.

Is it possible to create some sort of chatrandom tunnel to direct the AirPrint into the MikroTik router's network?

Thank you.

Turn off the routing on one of the routers, and make it a switch.

It might be possible to leverage IGMP Proxy or PIM to make Airprint discovery possible across layer3 boundaries.
But as already mentioned, the easiest and least error prone solution is to ensure that everything is within the same layer2 domain, i.e. change your secondary router's configuration from being a router to a bridged access point.

Btw: Ubuntu 12.04 has been EOL for a very long time, you should really move your configuration to a newer operating system.

The best way to solve this, make Mikrotik WiFi to bridge mode. No dhcp-server, no nat, all ports to one bridge. In the most of home installs its the best way to have one router as main (with internet connected) and all other devices as bridge/switch mode