For Beer, I've always put them in the secondary. Primary would have all the other stuff that might have been in the boil depending on what your making. So if your making a Vanilla Bourbon Barrel Porter or Stout you'll have the Vanilla Bean and what ever else went in at flame out. Then you'll rack off of those and onto the chips.
For Pepper mash I'd allow the primary fermentation, say 45 days, to run it's course. Yes, the active fermentation will be complete before then but to me there's just something good about the 45 day cycle. Then I'd process the sauce like I was going to bottle it but put it into a secondary with the chips for another 45 days and then process and bottle.
I haven't played with it any yet but I do have a bag of dark toasted chips standing by. Think I might get a bag of light toasted and try a simple mash and put half on one and half on the other and see what happens.
Cheers