I use 3/4 long "long johns" for that reason. Never liked multi layers in the boots, be it full footed long johns or calves lenght ones. Last time I got a calf long model and decided to give it a try, did regret it greatly. The "burns" I got due to friction were very painful and lasted days (syntethic long johns in tight race plug boots...)Base layers should be above the boot, the only thing you want in the boot is your foot and a sock.