You will need to set the cruise level each time you save a flight plan in FSC9, or you can manually edit the pln file and change the cruise altitude there, then save the file.
title=CYYZ to CYYC
There are times when you may need to manually edit the pln file anyway. PFE (or PF2000) dropped waypoints that were too close to the airport or too close together. PF3 does not drop waypoints; it just shows a warning. FSC9 will not allow you to delete waypoints from a SID or STAR so there may be instances where you need to edit the pln file to remove waypoints you don't want.
PS, but then what does the A/C profile do in PF3 if the Cruise Alt is set in the flightplan?
You can set climb and descent rates which PF3 uses for internal step-climbs and descents, but if you want to cross a waypoint at a particular altitude you should still set it on the waypoint page. The a/c profiles also allow you to set final approach speeds for different aircraft. Select the a/c profile when loading the flight plan.