Ok, now it's clearer what you meant.
Well, I don't know what other players do and I haven't played any Campaign Game yet and the scenario's instructions do not tell you which bots to use; however, they clearly tell you to use the Awakening's rules from the beginning if you play the Alternative History variant (page #18):
The Labyrinth: Awakening Expansion Rules, Player Aid Card and End of Turn Sequence are used from the beginning and throughout the Campaign
Rationale is quite simple: shuffling both decks together you could draw cards with new mechanics/effects immediately.
Following that train of thoughts, I'd say you should use the Awakening's bots only and, of course, use the Awakening's Event Instructions Table only, not any other home-made list.