I'm stuck at the point where Sam goes through the door and is faced with the guard walking around with the flash light, if I sneak up the two flights of stairs I get shot by the other guard or if i knock him out i still get shot

... Double Agent?

And it would help if you explained to us what level and what part of that level, please. We're not mind readers.

I think you have to use that remote thingy. Try waving it in the air and press some buttons. Should get you somewhere I hope