I've been puzzling this for a couple of months, and am wondering how Eventide will handle it:
Modulation effects fall into two categories – those which are applied pre-distortion (wah, phaser), and those which are applied post-distortion (flanger, chorus, trem).
It pretty much has to be that way; wah won't work properly post-distortion, and chorus won't work pre.
So; short of buying two ModFactors, what's the workaround? All I could come up with is if you could allow each of the two input/output pairs to effectively own an effect and route it a bit like two loops…