I would suggest trying both ways, but I don't know if it will matter much.
Doesn't your ear pick up the high frequencies to tell 'when' a note is? The French Toast won't noticibly delay the signal since it's working in the analog domain, and the fundamental that passes through the Boss won't be delayed. The lower octaves will take a moment to track, but the note's already got an attack on it by then. Another possibility will be that the French Toast accentuates the attacks of the lower notes as they enter if the French Toast is second...
You know what, I had the OC-2, and got rid of it later. I realized that the Super Octave must be the new OC-3. I hope it tracks faster than the old one. The OC-2 tracked better when I played guitar into it than when I played bass into it. I don't think the high freq stuff will hurt the Boss much. (Back in my day there wasn't no separate bass input, kiddies.)
Wait! I got it! Run the Boss first, but send the dry out to the French Toast?
I'm so confused...Nobody wants dry French Toast.