First of all, it's important to understand that each 12AX7 tube has two gain stages.
Tube 1a is common to both channels, it is the first (input) gain stage.
For the clean channel, Tube 1b and Tube 2a are simply bypassed.
When the crunch channel is selected, Tube 1b and Tube 2a are included in series in the circuit. These are all gain stages.
Tube 2b is for the tone stack (EQ controls)
Tube 3a and 3b make up the phase splitter to drive the output section.
Changing Tube 1 will have the most significant effect on the sound. Because of the high gain, it is important that T1 and T2 are "A" graded, ie least susceptible to microphony.