Boot cut jeans should just about skim the floor at the back of your heel. So, it doesn't matter what height your boot is, because you can't see too much of it.
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Shoes are gonna show when you sit, etc. So you just have to give them they eyeball test. The heel height really doesnt matter. I wear bootcut jeans w/ everything from ballet flats to 5.5 inch platforms and everything in between. Sandals to boots. They just have to look right w/ the pants and with the outfit and be appropriate for the occasion and weather, etc.
You can control the length by wearing or not wearing a belt and how high you pull the pants up and how tight you buckle the belt. And of course, you can hem the pants. Or use Stitch Witchery if you don't care that the topstitching will be gone.