Are you talking about bi-amping (splitting the signal up into high and low frequencies and sending those signals to two different amps and speakers) or re-amping (recording a dry signal and sending that signal back out through an amplifier)?
Depends on the effect. I like putting the effects on in mixing. That way, you can have a stereo chorus/delay/reverb that hasn't been funneled through a bunch of distortion and a 12 inch speaker.
I'd record the git dry regardless ...... then if it's FX that you like to have in front of the amp when live, then I'd put them after the re-amp out and in front of the amplifier. If it's mixing FX, then I'd put them in at mixdown like any mixing session.
The guitar input. The whole idea of re-amping is to have the recording take the place of the guitar in the signal chain. That way, you can get the performance with what ever sound the player is comfortable with, then feed the performance back through an amp to geta different (better, more appropriate) sound.