@prof Congratulations on your new gear. I think you'll like the improvements. You called yourself a sub newb in an earlier post, but IMO, your previous comments suggest you understand the principles just fine. So dive in and have fun.
My impression is that steeper is better for crossover slope, so probably 24 dB per octave is best on the CR-1. On the other hand, it might not matter all that much since your Thiel mains and JLA subs should both have good linear frequency response in the overlap region, even at 12 dB per octave. Easy enough to try both if you like.
As before, I recommend the Sound Doctor's sub setup instructions here (or see hardcopy with your CD):
http://www.soundoctor.com/testcd/Soundoctor_Test_CD_v2-7-2.pdf.
As for crossover frequency, here's a range of opinions. Sound Doctor says,
I suggest never going below 80, even if you think your speakers go down
to 40, or below. Even in a room where the existing "mains" have a pair of 12" drivers (each) you will get far better results if
you ... correctly cross them over at 80, (or higher) ...
The Thiel SI-1 instructions state,
Unless the main speakers are very small, it is
usually preferable that this setting not be higher than 80.
There's no explanation for Thiel's recommendation of 80 or below; it might be specific to some feature of the SI-1 or Thiel SmartSubs (probably not specific to Thiel mains because the SI-1 is intended to work with any make of main speakers). Alternatively, it might have something to do with staying well below the frequency at which the period equals the sub's group delay (about 120 Hz for JLA f112s). Above this point, the minimum timing error doubles to 720 degrees.
Finally, a team of audio pros working with JLA f112's and Thiel CS3.7s chose 100 Hz in this example,
http://www.soundoctor.com/studio/.
I decided to follow the Thiel recommendation (because I'm working with all Thiel components except for the subs). I selected 80 Hz as my reference but also stored preset configurations at 60 and 70 Hz for comparison. I can switch between these from my listening position with the SI-1 remote, but to my ears, they are indistinguishable. They all integrate seamlessly, and I couldn't reliably detect differences between these settings –– either in the highs or the frequencies surrounding the crossover setting. Still trying to test this.
I suggest you also consider settings somewhat above 80, e.g., 90 or 100 Hz. In fact, I spoke with a support person at JLA who helped an audio dealer install JLA subs, a CR-1 set to 100 Hz, and a pair of Thiel 3.7s. The dealer said it was the best sounding system he ever heard in his space. I would think your 2.7s should not be all that different from the 3.7s. Maybe I'll try up to 100 Hz, too. Can't hurt.
I found the Sound Doctor's Method B (p 4) for adjusting phase and level to be easy and effective. Rather than depend on my hearing, I used a sound-pressure-meter app, SPLnFFT (available for iOS and Android), to easily identify the settings for maximum cancellation.
Good luck!