From Cuenca, you will find buses, of the Cañar line, which can take you directly to the ruins. The last bus back leaves the ruins at 4 p.m. and the ride between Cuenca and Ingapirca takes around two hours.
From any point North (Quito / Baños / Riobamba / Ambato) you will need to get off the bus in a small town called El Tambo. There, it is easy to hire a pickup to take you to the ruins for $4 (15 - 20 minutes). I regretfully used the foulest public bathroom in my life in El Tambo - and I'm not picky.
If you're on the go, you won't want to visit the ruins carrying a heavy bag. The men in the small museum will kindly watch your bag at no charge (lock your bag all the same).
Maybe you've read about the Cañar civilization, which was one of the groups which joined (or were coerced to join) to form the Inca empire. The town of Cañar, which lies between Cuenca and the ruins has little to do with the ancient Cañar. Today's Cañar is mostly distinctive in the way women have pompoms dangling from their hats. You will see all there is to see in Cañar from the bus' window.
The Trans Canar bus company runs buses from Cuenca to the ruins (not the village which is 1 km away). On weekends, there is one departure at 9 AM. The bus arrives at about 11 AM and waits in the parking lot until 1 PM. The cost one way was $US 2.50 in January 2007.
On weekdays there are additional busses. The last return bus on weekdays is at 4 PM. If tickets are purchased from the ticket office in the Cuenca terminal, seats are reserved. If payment is made on board, seats may or may not be available. The bus stops frequently to accept additional passengers en routre.
There are several buses that make the route to the town near the ruins. Once in town, you can walk to the ruins that are located about 20 mintues outside of town. The scenery is lovely so it makes for a nice walk.