You need to use the CFS3 Mission Editor available from Microsoft. Open the mission file, select the flight you wish to alter, select the waypoint icon, and for each waypoint, use the up/down arrows to choose a new altitude, or type in the altitude you want.
Then save the file, or save under a new name, so the original remains intact.
Modifying an existing mission in this way is very simple. 8)
When you get more adept and turn your attention to altering spawns and spawn tables, you really do need to create new ones, because altering existing ones can screw up other missions.
The editor is quite simple to use - it's just Microsoft's guide that ought to be written more clearly.