If you need to stop, hit the brakes! That's it. Don't worry about the clutch right now (worst thing that'll happen is you'll stall the engine, no biggie.) And sorry for stating the completely obvious, but let off the gas! Duh :)
OK what to do with your feet? 3 pedals, 2 feet. Here's what you do. Your right foot works the accelerator OR the brake (one at a time, lol!) Your left foot only works the clutch.
Most of the time your left foot actually sits in the empty space to the left of the clutch. Why? Because we do not "ride the clutch". Unless you are actually shifting this moment, your foot should be off the clutch completely. There's a reason for that but let's stick to the basics :)
(by the way, it's exactly the same if you drive an automatic. Right foot works gas or brake. Left foot does nothing at all! Yes, I know that defies the logic of "2 pedals, 2 feet" - but ask a professional driver if you don't believe me.)
As you have probably noticed, manual transmission cars have engine brakes. If you let off the gas, the engine actually drags you down a bit. It's stronger in lower gears, right? That's OK, and it's actually useful.
If you're braking, when do you need to let off the clutch? Well, you know that you shouldn't pick a gear before a certain speed, like say you shouldn't take 5th gear until 35 mph. Well, if you're in 5th gear now, and braking, you don't need to worry about the clutch until you're below 35 mph. In the meantime the engine is giving a little bit of extra braking, not enough to matter, but it's OK. Once you get below 35, you should either downshift into a lower gear, or just shift into neutral.
Neutral! That magic gear in the middle that is no gear at all! It is your friend. When you don't want power or engine brakes, put it there and let off the clutch.
Let off the clutch. If you find yourself holding the clutch down for 5, 10, 20 seconds at a time... well, that's not ideal. That's slowly wearing out a part inside your clutch that's only meant to run for a second or two. Won't be a problem for years, but it's not a good habit, so let's leave that to Clutch 202.