Difference between net start MongoDB and mongod
You can always run mongod with a command. But if you decide to run mongod as a Windows service, in first step you need to set up a service by running mongod with --install option:

"C:\Program Files\MongoDB\Server\3.4\bin\mongod.exe" --config "C:\Program Files\MongoDB\Server\3.4\mongod.cfg" --install


Then, you can use net start/stop to use the installed service:

net start MongoDB