You probably figured out shifting on your own, but here it is: when you are in the forward position, you up-shift by lifting the entire foot.
You will be in the forward position when accelerating, so it it the most likely position to be in when you need to up-shift. Likewise, you will most likely be back when down-shifting, unless you downshift looking for more power.
The shifter should be adjusted properly and that means level with the peg or slightly higher. The position you are adjusting it for is the standing position, where you should be most of the time.
Here is a video talking about these points:
You have to practice and get used to shifting in all positions and all situations.
Also, to get really fast and smooth, you have to learn to flow and reduce shifting to a minimum.
The interesting part about the video above is that Semics suggests always using the clutch for up-shifting and not for down-shifting, which is contrary to most advice I have seen to date.
Here are my thoughts on that.
On a big bore four stroke, when you're releasing the throttle, you will get engine braking, which will then put sufficient load on the gearing mechanism to worry about using the clutch when down-shifting.
On a two stroke, there is no real engine braking, so indeed, you could downshift without using the clutch.
On upshifting, I mean if your throttle control is pretty good, you should be able to upshift without much clutch in the woods, at small revs that is. Likely for motocross, when the revs are constantly pretty high, chances for screwing up are higher, so you should probably use the clutch most of the time.
You don't have to pull the clutch in all the way - after you get accustomed to exactly where and how your clutch engages, you should be able to just pinch the clutch lever slightly - the idea is to take some pressure of the dogs and pegs during the actual shifting and for that, you don't need to completely disengage the clutch.
As you know, the clutch is made of many plates compressed together with springs. As soon as you start pulling the clutch lever (after the 8-10mm of play that it should have) it will start releasing pressure off the plates and they start to slip.