I usually lace them to the point that you lace all other shoes, tuck the laces in without tying them, and tuck my skinny jeans in. I also fold down the top part sometimes, depends on my mood and my outfit. I personally don't like the look of jeans overtop of high tops so I don't do it, but that is personal preference. You can also cuff your jeans so that you can see the entire shoe.
you can wear it different ways. the way gazillion said is one, that is how i wear them. my friends like rolling the bottom of there jeans so that you can see that they are high top shoes. you can also fold the tops of the sneakers down if you take some of the lace out.
I would wear the shoes over the jeans and wear a plaid/flannel button up shirt.
I usually just wear it without tuckin it in if that's what u mean.