It all depends on the final ranking/seeding, which is heavily influenced/determined by the conference championships. Whoever wins CanadaWest and whoever wins the AUS will be ranked 1-2 or 2-1, as it is unlikely now that the OUA team will suddenly launch into one of the top 2 rankings.
The University Cup seeding rules state that the three conference champs (AUS, OUA, CanWest) must be seeded 1, 2 and 3 based on the last ranking. The three runner-ups are then 4,5,6. #1 is in one pool and #2 and #3 are in the other, and the other three seeds are juggled to make sure that the two reps from each conference are in different pools.
So if Alberta wins CanWest and UNB wins AUS, they can't be in same pool, and therefore Sask is with UNB. If SMU wins AUS and Sask wins CanWest they'll probably move up in the final rankings to 1-2, and therefore they'd be in different pools, and Sask gets UNB again in their pool. If the rankings follow their current trend, UNB and Sask have to win their conferences to avoid each other in pool play.