I flew with my boots in a carry on bag, and I also managed to fit socks in to my boots, and quite a but of baselayers in with the boots also.
I bring a ski bag made for 2 skis, and pack that bitch full of clothes. It also has spots for boots....(which I used last trip). But yeah my sticks in there. Then my carry on contains the rest of my clothes and boots. My backpack carries my laptop, digital camera, hd cam, and chargers.