Most Airlines only allow crews to fly LNAV or NAV approaches from "data base approaches". If you modify the approach or construct your own then you cannot fly it below MSA using LNAV or fully managed modes.
So, if you select a particular approach or departure in your 737 FMC that contain fly over waypoints then they will already be correct and you shouldn't modify the waypoints or the altitudes.
Last edited by nitpicker330; 9th Jul 2012 at 11:39.