I have a 2002 A6 3.0L and have been trying to get it to pass smog emissions. It has codes:

17819 Secondary Air Injection System; Bank 2: Insufficient Flow
17831 Secondary Air Injection System; Bank 1: Insufficient Flow
I also had multiple misfire codes.

The cleared the codes and it has not come back for a few days. However the SAI monitor is not ready. I used the "set readiness" function on Vagcom Ross Tech VCDS and when I floor the accelerator on the SAI setting, the RPM's do not move at all.

How do I even start with troubleshooting?

 

First of all if you go through the readiness testing - flooring the pedal is only for the test program to set readiness. RPM should not move or barely at all (very normal). Just follow the on-screen instructions.
Now if the Codes come back for SAI, check the connection hoses between the pump and the intake. I've seen a lot of cracked, ripped and completely missing tubing from the pump to the back of the engine. Very simple and cheap fix if that is the issue. After that check your Pump for issues. Once that is fixed - rerun the test and make sure it comes back clean and ready.

In regards to misfires: See if those codes come back when cleared. There are tons of things that can cause this - including vacuum issues, coil packs and Sparkplugs. Since you already have the SAI issues - check all the hoses first, work your way to the engine (coilpacks/spark plugs)

Good Luck