If I'm fermenting in a tank that's larger than 5 gallons I stir infrequently until it reaches a certain gravity at which point I'm concerned about too much oxygen. I base that gravity off my intended finishing gravity. I try and stir until about 0.015 or 0.020 above intended finish. For example, if I want a finishing gravity of 1.000 I'll stir until 1.018 or so. I want to make sure it has enough oxygen to get through the bit of fermenting, when it's most likely to be oxygen starved, but I don't want so much oxygen that there's a bunch left over.
By the way, this .015 to .020 number may be completely arbitrary, but it seems like it's working out pretty well (I've made several hundred gallons this way). I've done it at .008-.010 before because I got to it late. It was fine. But it's better in the .015-.020 range I think.
For flavored ciders I usually rack onto that flavor (i.e. I rack from primary into a secondary container with vanilla beans). You must do it this way if you want it to taste like that thing would taste.
If you're racking onto a fruit and you want it to taste just like that fruit, you need to add both potassium sorbate and k meta or keep your cider really cold while it's absorbing the flavor so that the yeast don't wake up and start fermenting it. Fruits generally have enough sugar to reawaken the fermentation and send it back into a sort of semi-primary fermentation. It'll keep some of the flavor but it'll also taste partly like a wine made from say, pure cherries, would taste.
You can also rack the cider several times and get the yeast alllll the way out, but doing that runs the risk of adding too much oxygen, especially if you don't have the equipment/expertise. Done correctly, you also will not be able to bottle prime it this way because it shouldn't have yeast with which to bottle carbonate.
You can also go the pasteurization route.
By the way, this is all based on my experience - others may feel differently and I'd love to hear other people's thoughts here.