I am in the habit of using Shift+N to put a note beside the levers. Names are things like: "Farm1 Fill Inlet" and "Farm1 Irrigation Gat". Then I fill in the text with a description, and go mark the floodgate, door, bridge, whatever in the same way.
I construct the first control levers in the same rooms as my bookkeeper's office and manager's office (I put all non-demanding "nobles" offices in a row, so they are all easily findable).
I use color of levers to help clue me in when possible to the use (ie, microcline levers for water controllers).
And you can always figure out what a lever is linked to if you pay attention: just try to link the lever to something. Whatever it controls will NOT be available on the list. IE, if you think it controls a floodgate, try linking it to a floodgate. You can walk the list of all built floodgates in your fortress, and if you skip any, you know it is linked (note that DF has an issue with displaying the actual item it is showing, so it can take some experience with understanding what item it is ACTUALLY supposed to be showing).
Of course, figuring it out can take a long time in a well developed fortress. But if you are worried about WHICH lever controls a door or floodgate that is holding back the magma, it is well worth taking the time to check rather than just flipping it and seeing what happened (not as dwarvenly, of course).