Best thing to do is look at a map first, decide which rides you want to go on and word out a route. Alton Towers is huge geographically so it's not a case of "I fancy a ride on Oblivion now." Because if you're next to Air, that's a 10 minute walk.
Alton Towers is roughly a crescent shaped park with the skyride linking each end together (you can walk across the valley, but that takes a long time). The entrance is in the middle of the crescent. I usually find the best plan is to start at one end and work my way round to the other end. So you could go straight to Rita and Thirteen, then walk back towards the entrance doing X Sector, Spinball, then move on to Mutiny Bay, Katanga Canyon, Duel and Forbidden Valley.
Alternatively, you could go straight to one end, let's say Forbidden Valley, take a skyride to Ug Land to do Rita and Thirteen, then work your way round.
But usually, however you do the park, you'll get to do everything you want to (unless something gets closed of course).