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Is it before rolling for mission/deployment? Or after? I cannot for the life of me seem to find it in the BRB.

It's in the actual set-up rules on page 92 and 93 of the rulebook. It's decided as part of the roll for deployment.

Thanks! So it's actually the very LAST roll that happens. We did this incorrectly in my last game--we did it before anything else. It could definitely matter, too. You may want a different edge of the board depending on mission type/deployment type.

Depends on what you mean by "last"; the last roll is usually to Seize, if player 2 wants to. Just to review real quick:

Roll mission and deployment type.
If Seize Ground, place objectives.
Roll for choice of table edge/going first.
If Capture & Control, place objectives.
Player who chose side deploys army.
Other player deploys.
Infiltrators deploy.
Scout moves.
Roll for Seize the Initiative, if desired.