When I played the original Logic file through my MOTU 828 MKII + Focal monitors, I heard the click in the audio file and vice versa.
I think took Fastfourier's suggestion and bounced each track separately while muting the other, and created a new Logic project. When I imported those new files and panned them, everything seems to be working as expected. I didn't have my headphones handy, so I couldn't make absolutely sure I didn't have any cross talk going on, but when I put my ears up to each speaker, things sounded right.
I then unplugged my MBP from my 828 and opened up the new file in QT. I used my iPhone headphones to monitor playback. Things sounded much better than they did before, but I did faintly hear some of the audio track in the click. I didn't hear any click in the audio track, though, which is the most important thing. If it was there, the music overshadowed it. Maybe all I'm hearing, though, is very faint cross talk because of my MBP's built-in audio?
I guess the thing I have to do is monitor using my MOTU and use headphones to be 100% sure things are working as they should.
If so, the question remains. What was I doing wrong the first time? I'll be making a lot more backing tracks with a click track, so I want to make sure I get things right from the start.
Thanks!
Jeff