How to save engine files once changed?

CTRL+R to reload the vehicle.
That will also load your changes.

 

#1 rule:
Do not overwrite the original files.

Create a new folder in your documents/mods/unpacked folder and call it whatever you want.
Then create a folder called vehicles
After that xreate the folder matching the name of the vehicle that your are modifing and paste the engine file from zip to the created folder.
Preferably change the name of the jbeam file and change the name of the part itself. Save the jbeam just like any other file (ctrl+s) then you will see the part in the vehicles selector ( after reloading the vehicle ctrl+r) select it and then tab over to your engine file and put apply your changes. After saving and reloading the vehicle you should see the changes in game.