My suggestion would be to go from the full range output of the F-1X to the input of channel A of the SF-2, and then out from the ouput of channel B on to the power amp. For me, I tend to think that the tube and the bass, mid, treble of the F-1X do the preliminary tone work, and then the SF-2 does the more detailed tone shaping; so that's why I run the instrument into the F-1X and then go from there to the SF-2.
It does seem that going to the SF-2 first would also be a reasonable approach as far as tone shaping. However, it does seem that signal gain balances will need to be accounted for since you will be changing the input signal strength that the F-1X sees. Thus for purposes of controlling signal gain along the path, I like having the F-1X ahead of the SF-2.
A post I made three years ago
here talks about setting the SF-2 up as a three channel mixer.