I live in booties with skinnies and straight legs all winter, and I tend to wear super skinnies (for me, anyway) right into the bootie. Looser skinnies and straights I either wear over the boot or -- my preference -- cuffed, exactly as Lisa described -- to above the bootie, and when the cold weather sets in, always with socks. The socks do show but then we are all in knitwear so it works somehow. If it's a refined look, then a refined sock; if not, then a slubby one.
I do think that comfort has to be number one. Second is ankle opening. A little is fine, too much and you get flower-pot effect, with your leg looking like the stem growing out of the boot-pot. And you look like you have delicate ankles, so it might be a challenge. (I, alas -- or hooray! -- do not.) I would follow Angie's guidance on brands for sure.
Good luck! I hope you find the right pair.