I found some rust in the inside of my tunnel....I'm thinking of pouring some paint down the access covers...is there a better way to deal with this?

Use phosphoric acid to stop the rust from breathing, many products are available.
This treatment turns the rust black, and prevents O2 from penetrating the surface and allowing the rust to spread.
The acid is sold in many forms, POR sell it, lots of products out there.
Its the consistency of water, so it can be sprayed in lots of places with long wands.

So,
Get that stuff, go to eastwood.com and get a wand, or buy a garden sprayer (a small one) and use that with a wand.

The wand with a wide fine spray mist will allow you to reach into the tunnel via all the access holes and coat all of it.

Rich