There are many different key setup configurations people use. You should use what you feel most comfortable with. Though an absolutely horrible key setup (one that puts your fingers in awkward positions) may affect your game slightly, overall, you won't find "improvement" because you're using a better player's configuration. There are two main configurations that people tend to lean towards.
1. W or 2nd mouse button - forward, S - backward, A - strafe left, D - strafe right, spacebar/2nd mouse button - to jump, and 1st mouse button - to fire.
2. Z - strafe left, X - backward, C - strafe right, 2nd mouse button - forward, space bar - to jump, and 1st mouse button - to fire.
My personal key setup looks like this: W - forward, A - strafe left, D - strafe right, S - backward, 1st mouse button - to fire, and spacebar - to jump.
I also bind shift to switch to rocket launcher, and the 2nd mouse button to switch to lightning gun. If you do not know what key bindings are, it will be explained further later on.
Again, two of the most important points in selecting a controller setup are efficiency and the ability to hit critical keys together. The point of using the mouse in quake is to take advantage of its precision and speed in turning and looking up and down. Thus, using the mouse's movement axis to strafe basically defeats the entire purpose of the setup.
Keeping this in mind, use the x-axis of the mouse to turn, and the y-axis to look up and down (there is no particular advantage or disadvantage to the "invert mouse" option, it's just personal preference), and
bind separate keys to "+moveleft" and "+moveright" (whether on the keyboard or two of the mouse buttons). It doesn't really matter which keys you use, as long as you can look around and vertically, strafe, move forward or backwards, jump, and fire at the same time.
As intimidating as this may sound, it'll soon become second nature to you, and the benefits of "mouselook" will be quite apparent as you continue to play.