I am not positive that this applies to the 1900 but sometimes Beech autofeather systems do not test properly on the ground because the torque doesn't get down to 200 pounds at idle. If this is the case lift the power lever into the beta range to get the torque down below the 200 pounds.
As for autofeather test in flight it is very simple: Make sure you are in VMC, put the power levers high enough to arm the autofeather, and put the condition lever to cutoff. Do not use the firewall shutoff valve as this can damage the fuel pump. Engine should feather very rapidly.
If you do not feel comfortable shutting down one engine for a short period then by all means DO NOT do this. But please speak to your training department about this as you really should not be flying people around in this case.
If the right seat pilot has air gyros then the aircraft must be flown from the right seat during relight as the checklist calls for avionics master off. If only the standby gyro is available it is usually better to have the right seat pilot fly anyway.