You can actually put two getin waypoints onto a vehicle, though its awkward. Use the SHIFT key to gain access to the vehicle below the waypoint. It can be very difficult to get access again to the second waypoint as you say.
It may indeed be better to script it. Fortunately scripting is easy. Look into Tutorials - Scripting in the Ed Depot. You could do worse than start with Johan Gustafsson's Scripting guide. Scripts are just lines of text that give the game instructions. They can go in the init field of a unit, or in triggers or waypoints, or in seperate little files. The most famous line of script in the whole game is this inflame true, which goes in the init line of a fire to make it burn.
There are several versions of the Official Command ref in the Ed Depot. The version at References - Commands includes comments on some of the commands. The downloadable versions are in Tutorials - References - Command References, which also includes the invaluable Unofficial Command Ref Guide. What all of these give you is list of all the commands that exist and short explanation of each one.
Now, having said all that, lets answer the question.
Name the car .... car1
Name the loon .... civvy
Here's the script ... syntax not guaranteed, check it in the command refs mentioned above. I also don't think its a particularly good solution, hopefully somebody will come up with a better one. Anyway, its better than nothing. The script should go in a script file, lets call it getin.sqs The tutes will tell you what that means, how to create it, and how to start it at the appropriate moment. (basically you put [] exec "getin.sqs" in the on activation field of a trigger)
; this script gets the civvy back in the car after the cutscene
#loop
civvy doMove getPos car1
~2
?civvy distance car1 < 1:goto "getin"
goto "loop"
#getin
civvy moveInDriver car1
exit
The biggest problem with that script is that there will be no animation of the guy getting into the car, he'll just teleport into the driver's seat once he gets to within 1m of the car. However, it will at least make your mission work, which is the important thing. Details can be sorted out later. Or now, if somebody posts a better solution.
Oh, and lots of people still use 1.46. It's superior to Resistance in several respects. I use 1.91 for some things and 1.46 for others.