Tony, I often do the trip from Warrandyte to Eltham in my canoe or kayak. If you drive into Warrandyte from Templestowe you get to the first round-about then turn left straight after it. Goes down a little slope into a car park, that's right near the river. That's where I often launch. It's just a matter of sliding it in where you feel comfortable off some rocks. You then paddle left, downstream and your first set of rapids is about 20m away, under the big bridge in Warrandyte. A series of similar rapids follow for the next several km. You will have to make a decision about how you get picked up downstream. I get picked up by the missus at either Pound Bend (see Melways) or at Fitzimons Bridge Eltham. I'm lucky beacuse I live 10 minutes away. It's easy for me to get dropped off then get picked up. You may want to do the two car thing. Anyway, If you want to paddle from Warrandyte to Pound Bend give yourself about 1hr+ of steady paddling. This run has good rapids every few hundred metres. If you want to continue past here, you can get picked up near Eltham. (Fitsimons bridge) This lower section has fewer but bigger rapids. It is deeper calmer water. And this stretch from Pound bend to Eltham will take you another 1.5 hrs approx. It will be more more work too because there's less flow - some day less fun.
p.s. Wear jackets and helmets, don't go during floods, take a rope to help you retrieve a canoe from the bank if it goes in, if your doubtful about taking on a rapid you can always walk around it, when you go down a rapid guide the canoe into the V of calm water that extends deepest into the rapid. This is generally the smoothest ride through it. Just a few tips. Hope it helps. Mick