Susand, I think skirt length should be based more on your height/what's flattering than on your footwear. I have most of my skirts hemmed to the same place (just under the kneecap) and wear them with boots, heels and flats alike. With my boots, a few inches of knee are visible, but I just wear black hose (to match my boots) and don't worry about it.
So, if mid-knee is your "sweet spot" I'd hem your skirts to there, and try to pair your boots with hose/tights to create that uninterrupted line, just like the other ladies said.
If you really love the boot-into-skirt look (ie, no actual leg showing), then you might need a pair of over-the-knee boots to do it with! I LOVE that look myself, so a pair of super-tall boots is definitely on my list :)