The standard course of the parade and the races is from Bacino di San Marco along Canal Grande to Rialto, with finish at Ca’ Foscari.
Don’t forget to pick up an official program at the tourist office at the San Marco square. It gives you all the timings, as well as information about the boats and the teams. The program keeps being updated, so if you want to be sure about the timing, I suggest you check the official website before you leave.
The main events of the Regata Storica take place on Sunday. However, if you are around, you should also attend the presentation of the teams and the blessing of the gondolini on Thursday. This is mainly attended by the locals, who come to cheer for their friends and family who were able to qualify for this race.
As this is a major event, both celebrated by locals and by tourists, you should expect that it will be very crowded around Canal Grande. Finding a good place to watch the whole event is the only thing you might have to worry about.