As I recall, having been on it once or twice, it followed the usual route for passenger trains going to or beyond Ballarat, i.e. North Melbourne, Footscray, Sunshine, Bacchus Marsh etc. But I believe it sometimes went via North Geelong to Ballarat, so it would diverge at Footscray. Not aware of any turnouts before North Melbourne.
In those days the Overland was notorious for late running, and even today it is known colloquially as "The Overdue". I found an old website saying that the Up was timetabled to arrive at Sunshine at 8.40 am, while the Down Daylight left there at 8.57, thus giving pax 17 minutes for the transfer if on time. Don't know what happened when the Overland was significantly late, but can't imagine the Daylight being held for more than just a few minutes.
A bit more info here: https://www.railpage.com.au/f-p2034887.htm
As an aside, I also found a reference to the Overland once going via Mt Gambier, back in 1954, due to an obstruction on the main West line.