All right, here's how it usually works -- most tour groups do almost the same thing. This is the basic weekend tour, starting from and returning to Cusco:
First, you'll catch an overnight bus from Cusco to the city of Arequipa. The buses are pretty comfortable, as long as they have heat -- ASK! You'll be cold if you don't! Also check to make sure that the bus has a restroom! You'll arrive in Arequipa early the next morning and probably have an hour or two to walk around and get breakfast before starting off for Colca Canyon.
Then your tour will get into another bus, or maybe a van, for the five-hour ride to the town of Chivay – a tiny little town, but the closest inhabited area to the canyon.You'll spend the afternoon in Chivay -- go to the hot springs (this is about $5 and is included in some tours and not others). You can also walk around and meet up with your fellow travelers at the Irish pub right on the "Plaza" in the center of town. This is a cute place where you can play pool and drink Arequipena, the local beer.
The next day, you'll head out for the canyons, stopping at several different points to admire the view. The best place is where the condors circle around (especially if you get there early enough in the morning). Absolutely incredible -- great photo opportunity. You'll have an hour or two to walk around a bit here before heading back to Chivay. From Chivay, you'll be back in Arequipa for dinner, and then it’s another overnight bus to Cusco!
This is quite the whirlwind tour, but it’s definitely worth it. I wish I could have spent more time in the Canyon -- if you have more time to spare, I'd recommend staying another day or two and hiking around. Arequipa is also worth a longer visit -- it's a beautiful city, much like Cusco, but less touristy, and many say it’s more beautiful.