Hitting "E" then the number of the engine, 1 or 2, switches focus to that engine, and then all engine commands (including your throttles) relate to just that engine until you hit "E" on its own again.
So, for example, to shutdown just Engine 2, the sequence is E, 2, CTRL+SHFT+F1. Then hit E again (or E, 1) and you're back in control of Engine 1.
HTH
- Voodoo