Shift where ever you feel comfortable. For normal street riding, 4000-5000 works. I putts around at 3000 at times. But the faster you want to accelerate the later you shift.
Downshifting? For puttsing around the street, when you're rpm's start dropping lower than you want, pull in the clutch, shift down, and slowly let out the clutch (just in case you're not donig a good job matching engine speed). Yeah, that's the other thing, you want to anticipate your engine speed. I don't roll all the way off the throttle, I leave it cracked just a bit.
For high speed, it gets a bit more complicated. You can still use the same technique, but matching engine speed is more important. Pull the clutch in, blip the throttle, and let the clutch back out. It take spractice. I wouldn't worry about that just yet.
If you're "catching in neutral", assuming there's nothing wrong with the bike, just push a little harder. It should be one upshift from first to second.