[cayuse]

short answer is:
Once you stop, you should be in 1st gear, pulling on the clutch and using one of the brakes. I was taught to use the rear brake (right foot); it gives the throttle hand a rest.
You shouldn't need to engage the throttle at all. If your engine dies with the clutch pulled in you need to tune the idle; maybe it's simply set too low.
Good luck!