How to prioritise quaternions over transforms?

I am confused about how to properly combine transform.position, transform.rotation, and quaternions so that they dont override one another.

I have a spacecraft flying in a tube with:
rotation around centre of tube by angle (Blue,1)
change radius of rotation around centre of tube(Green,1)
WASD left-right-up-down strafing(Green,2)
mouse looking for aiming(Red,3)

How do i construct the script?

A/ set craft.transform.position at centre of tube
B/ Addition of Quaternion.RotateAround on top of A/transform position, how do i use Radius and Angle to control the plane flying in a wheel fashion inside the tube using RotateAround, and added to TubeCentre.transform position?
C/ add WASD strafing Transform.Position changes on top of step B
D/ add mouse look on top of step C?

Keyword: how to use quaternions, when to use quaternions