I started a few months ago. I generally use both brakes and progressively work down the gears as I slow down. You could do what you said and slow to a near stop on just engine braking, but it won't engage your brake lights which puts you at risk. So even if you're planning on engine braking the whole way make sure you are at least lightly pressing the brakes so the lights go on.

You could also do the other thing you said, pull in the clutch and jump all the way to 1st as soon as you start braking, but it could get you into some trouble too. I ride a 350cc bike with short gearing until 4th. The first 3 can comfortably get me to like 8, 15, 25mph. My 4th can take me basically to max speed and 5th is an overdrive. So say I'm coming to a red light so I rapidly go down to first because I plan on coming to a stop. Light turns green before I stop, I release the clutch and twist the throttle, and uh-oh I potentially damaged my engine because I just redlined it. If I remember I shifted into first I now have to figure out what gear I should be at and fumble to quickly reach it so I can accelerate. Both scenarios could be avoided if I just kept shifting to the correct gear for my current speed.