You can adjust the waypoint altitudes on the flight plan page. See the User Guide pp. 83-85 for more information. In most cases it is not necessary to adjust the altitudes for the climb phase of your flight plan. PF3 will show cruise altitude for your first waypoint but this does NOT mean you will be at cruise at your first waypoint. PF3 will simply provide you with step-climbs until you reach cruise altitude. You can adjust the altitudes for the climb phase if needed but this is rarely necessary. If you are flying a fully loaded heavy you may want to level off for part of your flight before continuing to climb, and you can configure that on this screen.
If you adjust any of the altitudes for the descent, you need to carefully review the altitudes of the nearby waypoints (including XXX waypoints) to see if they need to be adjusted as well, because PF3 does NOT automatically adjust the altitudes of the other waypoints. Hover your cursor over the waypoint names to see the distances to nearby waypoints, and adjust them if needed. If you have yourself descending 10000 feet in 10 miles, that is what you will get.