Rob, I think the area of the RBG closest to the Bruce Trail is the Rock Chapel Sanctuary, which appears to be quite a distance from Bayview. For Bayview, you can park at the RBG Headquarters, on Plains Rd., in Burlington, or go a bit farther along Plains Rd. to the Laking Gardens. There's a pedestrian bridge near here over the mainline, and the lower end of it also affords some good photo opportunities. Alternately, you can turn left off Plains Rd. before you get to the Headquarters Building, onto Spring Garden Rd., and follow this road, which dips down to cross a Bailey Bridge below Laking Gardens. The bridge may be closed to vehicular traffic, but you don't need to cross it anyway. Continue along the road to your right, upgrade, where you'll reach a parking lot, which is at the bottom of the aforementioned pedestrian bridge.
To get to Bayview itself, you'll need to cross the Bailey Bridge, then walk up the road, under the overpass for the tracks. The entry road to Bayview will be on your right, although this area is private property and is well-signed. Be extremely careful in this area, as Bayview is the busiest railfanning spot in the country, and trains drifting through here can be very hard to hear until they're almost on top of you.
If you want to do some walking, there are lots of pathways through the various parts of the Gardens. The Rock Gardens are my favourite, and are within walking distance from Bayview. Simply continue up Valley Inn Road from Bayview: you'll come to York Blvd., and the Rock Gardens are across the street and to your right. There's also a tea house there.
Wayne