I've used AD in MOUSE (for tracing and age), but haven't used it in 1D. In MOUSE for tracing, I felt like I had to take the strategy of setting it up first just to do something very simple - like a single source trace - just to make sure I populated all the correct dialog boxes.
There's some more documentation in [i]MOUSE Reference Manual (Pollution Transport)[/i], in Section 22.2 around PDF page 108. Not sure if there's an equivalent in the Mike 1D manual, or if the MOUSE pollutant transport manual covers the AD part of 1D.
I'm not certain, but I seem to remember needing to add explicit water quality boundaries to each hydraulic boundary (e.g., where the water comes from in my model) even if they were zero, which is implied in the discussion in the pollutant transport documentation in the section on boundary conditions. You may have tried this already, but it may be helpful to make a super simple model with half a dozen elements to make sure it's working like you expect.
