I don't have either unit but I took a look on the API site. The A2d has an insert point where you can loop out to other gear, ie. your compressor, before hitting the digital stage and leaving to the 003.
You can use a patchbay for anything but it isn't needed. If I am reading correctly, all you need is a "Y" cable to run out and back in as in any insert situation.
So the signal will travel A2D Pres->Out to Compressor->back to A2D for conversion->SPDIF Out->003->PTLE.
From the site:
"1/4" TRS insert to the A/D converter. This allows the A2D to have external analog processing devices inserted in the audio chain (EQ, compression, etc.)"
The "insert" on the A2D is not a send-return insert. It's just an input jack that goes direct to the converter. You would insert other gear by running the signal out of the XLR outputs, to the other gear, and back into the 1/4 inch "A to D Input" jack.
I don't have the model with the word clock option. I believe this is so you can clock the A2D from another source.
I use the A2D through SPDIF to the 003. When I'm tracking with it, I make sure to set the protools session hardware setup to clock from SPDIF instead of internal. Then when mixing, set it back to internal. The word clock option would allow you to clock from the 003. This would only be helpful if you're using the A2D and the 003 pres at the same time. But having said that, I've used both at the same time, clocked to the A2D through SPDIF, and it all seems to work fine.