For cycling the standard procedure is to wear cycling shorts underneath everything else. If its warm then just the bike shorts. For cooler weather, I have lycra leggings with the crotch pad built in. Another option is cycling shorts under long pants without an big crotch seam. Like these. Even colder weather, long underwear, snow boots and flat pedals. That's getting into full-on winter cycling with maybe studded snow tires and etc.
For running in cold weather I have wool leggings. They'd probably be fine for cycling (with cycling shorts underneath), but I usually don't bike when its cold enough to need them - under 25 degrees or so.