Like the guys have said, there's a lot of different options. Overpants, regualr pants.. In the boot style, or outside the boot style. If you arent sure what you want, id suggest just going to cyclegear and trying some stuff on, and seeing what works for you.
For short, in town trips, I have a set of kevlar riding jeans. They have armor in the usual places, are plenty comfy, and dont leave you looking like a power ranger if you ride somewhere to eat.
If i do anything more than just a ride to work, or down the street for whatever, I have some ADV themed MX style pants I wear, called MSR explorers. They're in the boot style, which I really prefer. I wear full MX style knee pads inside the pants, and my boots help keep them in place.
Its all personal preference
You should probably just try some stuff on and see how it fits. Maybe some more members will chime in here with what they use, etc.