This might sound like a smart ass response, but it's
NOT!
I prepare for engine failures in the Simulator in
EXACTLY the same way that I prepare for engine failures in the real aircraft. I fully EXPECT that an engine will fail before V1, and have a clear mental plan of the actions required for a Rejected Takeoff. After the V1 call, I then fully EXPECT an engine failure between V1 and the critical Altitude, and have a clear mental plan of the actions required for a continued Takeoff.
When the failures don't occur, I then fully expect that they will on the next flight, and today was a bonus.
The Simulator is intended to simulate the real aircraft. It certainly emulates this procedurally, although often-times the fidelity leaves something to be desired. If you don't already have contingency planning, and a mental plan, for engine failures in day to day flying in the real aircraft, may I suggest that you set about developing one? This contingency and mental planning is then easy to carry over from the aircraft to the simulator.
Regards,
Old Smokey