I'm having a hard time manually focusing my Nikon d40.any advise?

And every time i try to focus is automatically, it just makes a clicking noise, like the shutter is broken or something

It sounds like you may have damaged your lens in some way.

You can use the electronic rangefinder in the viewfinder, but make sure that you have the camera and lens in the manual mode, otherwise you can damage your camera and lens.

Look on page 28 of your user manual to learn about the rangefinder