What you have to do to shift smoothly is anticipate the amount of time it takes for the RPMs to drop before releasing the clutch. The drop in RPM from 1-->2 is like 1.2k RPM so if you try to shift quickly you slam the diff into the undercarriage. Either 1)slip the clutch moar or 2) Clutch in...wait...wait...wait...wait release clutch. Eventually it becomes a habit and it's easy to drive smoothly but it's definitely something you actively have to learn.
I've found that the phrases "clutch in" and "clutch out", if said slowly, are the appropriate amount of time for shifting. While saying them your foot should be moving, either on or off the clutch.
This is for granny shifting mind you.