Just a matter of key combinations:
Use Shift-1 then hit E for engine #1 and shift-2 then hit E for engine #2.
If you land with #1 dead and you want to shut off #2 press shift-2 then E...engine #2 shuts down.
In reverse:
Press shift-1 then E...engine #1 starts. Press shift-2 then E and #2 starts
then... (very important) after both engines are running press Sfift-E to select both engines for throttles use. If you don't, only only one engine will respond to throttle and round and round you go.....hope this helps.

Of course hitting E will either start or shut them both down.