So I found this John story and thought I'd post it here :
Examples of how co-fares work
For GO Train riders without a default trip:
In the morning, on Oakville John's way to work...
He taps on when he boards the Oakville Transit bus to the Bronte GO Station, and the Oakville Transit fare is deducted from his card’s balance ($3.25).
Before boarding the GO Train, John taps on at Bronte GO Station and pays the minimum GO fare.
When John taps off at Union Station, PRESTO’s smartcard technology recognizes that he should be credited for part of his Oakville Transit fare ($3.25-$0.65=$2.60) , and his GO fare will be reduced by the difference (GO fare-$2.60).
In the evening, on his way home...
John taps on at Union Station, and the minimum GO fare is deducted from his card’s balance.
When he arrives at Bronte, he taps off, and the remaining balance of his GO fare will be deducted from his balance. When John taps on his connecting Oakville Transit bus at the station, the co-fare is deducted from his card’s balance.
Also posting this for future refence to those who have the same question:
From
https://www.prestocard.ca/en/StaticContent/FaresTravel/
Tap the PRESTO payment device each time you board a bus or at the station before you board your train. Tap again when you exit.
GO Transit fares are calculated based on distance travelled. If you forget to tap at the end of your trip, you will be charged the fare to the furthest destination on your line. Your card will be charged automatically the next time you tap.
You have a 2.5 hour window to transfer between GO Transit vehicles with a $4.85 discount. Your transfer is recognized when you tap onto a bus within 2.5 hours of your first tap.