I assume you mean the large "pipe" with the hose attachment?
Its actually REALLY simple. Just plunge it into the gravel all the way to the bottom glass. This will start to pull up the gravel and the muck as the water flows into the hose... the gravel being so heavy will fall down again while the lighter detritus will be removed. When you are satisfied with that spot, move to a new spot and repeat. That's for a "deep" clean. If you do it regularly, you don't need to wait for long in any given spot before moving on. If you don't get everywhere, don't fret. Get it next time. As you run the tank for a while, you'll start to figure out where the majority of the gunk builds up and can focus more attention there, and less elsewhere.
Dig the wide end right down into the gravel; that's it.
All the 'mulm' will go up the pipe into your bucket and the gravel will fall back down. If you have a fine gravel, you might find a lot comes up the tube and 'stcks'; if that happens put a finger or thumb over the bucket end of the tube to stop the syphon for a second and it'll drop out
Once the dirt has stopped coming up, lift the tube up a bit and move onto the next area.