OK, you have a choice. Yes, in manual I set the ISO first, then work the shutter speed or aperture to my liking to get the correct exposure.
OR, If you like what shutter speed and aperture you have chosen, you can then choose auto ISO and your ISO will change to give you the correct exposure for the shutter speed and aperture you have chosen. BUT, in a way, you are now allowing the camera to make a decision on ISO, depending on the scene, the camera may pick a very high ISO. This, as you know, could lead to a lot of noise in your image.
IF, I am shooting in manual, I like to make ALL the decisions for the camera, ISO, shutter speed and aperture.