I got it!
I was able to run some sweeps and then poke around in Workshop and figure out the workflow. I had to look in the Quick Start guide a few times, but I think I've figured it out.
I ended up using Coneq PE1 to make a file that helped me some. I made two filters, one is an 80Hz High Pass Filter, I don't have subs right now and still have the factory speakers. The other filter is a High Shelf at 5hz that I initially set to -5db to keep the APL1 from clipping the inputs of the 800PRS. I eventually wound up setting it at -15db. I'll probably break out my O'Scope and do some testing with tones to find the right amount of cut. Being able to combine the two filters into one file is mighty handy.
Back in Workshop I built a project default that includes the Mic calibration file, the file from Coneq and the mp1 curve as my targets. I did 250 sweeps with each side playing, moving the mic around. It looks like if you setup the project default then Workshop automatically applies them when you are done recording, nifty.
I had music playing when I loaded the settings into the APL1 and it was fantastic when everything just snapped into focus. The highs were much quieter than I expected. I ran another round of sweeps, applied the changes and BAM! That put a HUGE smile on my face.
Now the Car doesn't sound at all like it has factory speakers on very little power. It sounds like I've put a LOT more work into the stereo.
I am curious about something that I didn't think to test while I was in the car. When I make a change to the file in Coneq, then save it over the one I'm updating, does Workshop automatically see those changes when I click "Calculate" in the lower right corner of the main window? Or do I have to manually reload the file?
I'll take some screenshots and see if I can'y put a click-cy-click walk through together to see if I'm missing anything and to help others out.
Based on my experience today, it was totally worth the effort to figure this out!