12" toms really are not problems they are just exact. The 12" tom is the "perfect" dimension so they really only have (1) voice for tuning that is right unlike other toms. A 12' will only sound like a 12". Most times we try to tune it too high especially when it is the first tom (say in a 12", 13", 16" setup) or if we have been previously condition to that standard setup. Treat the 12" tom like Middle "C" on the keyboard and make every other drum cater to it. The distance between your snare, 12" tom, lowest floor tom and your kick are the foundation fit any other drums around/between those. So in this case... the tonal order should typically be 10"-rack, aux snare (?), main snare, 12"-rack, 14"-floor 16"-floor, kick.
Yes, as Sticks' said the isolation method is the best start.
Let me add to that by saying you should tune to the lowest true fundamental note that 12" can get sounding good then "tune up" to the highest it can get which will be probably no more than a half turn up. not a quarter turn but a half. Also most important is to tune with a mallet to get the purest tone and most sustain... sticks give too much attack when tuning.