As you know you cannot/should not build waypoint into a datbased STAR or SIS or DP If, you have a string of wpt as a . . . transition say then the aircraft will descend to the next constraint say: 4,000/Nicky - you will have a lower altitude set say 3,000 alt, so the aircraft will level out at 4,000, fly past the waypoint, then continue descent to the next constraint, if any, and so on all the way down to your selected altitude.
Same for the climb, the aircraft will be at your waypoint at the desired altitude when you have alt constraint on it. You can modify this by entering AT altitude, NOT ABOVE altitude or NOT BELOW altitude, which you would plug into your FMS, prior to departure - or it would already be in there as part of the Descent/Climb/STAR/SID/WHATEVER.
If you are receiving ATC Radar giving you alts (up or down - Dep or App) then you would naturally, clear the constraints, or disc AP or just clean up the box and leave in the approach.