How do you calculate your settings in manual mode(5D mk3) with a speed light?

I use manual mode all the time and am quite good at getting the settings correct ApatureXshutter speedXISO and look at the bottom for the metering to be center +or - 1..
But when I have a flash on it does not seem take the flash into account or am I missing something? I know there are different scenarios like bouncing flash. Please help.. Thanks

It won't take the flash into account, that is just a lightmeter to give you an idea of the ambient light. Are you planning to use the ambient as part of the lighting, or do you just want the flash?

If you want the ambient to be used in the exposure, then set your exposure as normal on the camera, exposing for the ambient. Set the flash to ETTL and let it do its thing, it will sort out it's own exposure based on the ISO and aperture you have set on the camera. Shutter speed doesn't affect the flash (other than synch speed) so you can balance ambient and flash partly with shutter speed to adjust the ambient and FEC on the flash.

If flash is intended to be your primary illumination, then just set as above but set the camera so the ambient doesn't add much overall.

Remember to set HSS if your shutter speed is going to be over the synch speed.