Mixing 8-string guitar with Bass

Automation.

This is what I'd do. Different eq's for parts that are an octave lower and those that are in unison.

I play 8-string too but haven't recorded with it yet. I'll probably be going with bass that's an octave lower on my own stuff, but in band stuff we'll probably be going in unison when I play the lowest notes. I doubt our current bass player would like to adapt to a new tuning, since he's having trouble with adapting to tunings different from standard BEADG even now.
 
okay to clear up issues, I have a 4-string bass tuned up half a step, and my 8-string guitar is tuned down half a step.

For parts that are on the lower 8th string, I play in the same octave as my bass guitar, but the sound settings that sound good in that style of playing sound odd when I play "normal" chords on the upper strings.

that's my problem, since I'm trying to get a consistant sound on the whole track.
 
if that is the case, the the 2 options I see are:
1) automate or reamp each section with different settings,

or if that still sounds un natural, than you only choice is to

2) change the arrangement of your music. maybe the 2 styles you are attempting to combine just dont go together.