Hi Pat,
In Alpha Setup 2 and 3, there is a secondary mode key (referred to a 'Scale mode key' in the "A note about Scale and Tonic controls" diagram on p12 of your Alpha Quick Reference guide) which gives you access to the different controls which change the scale of individual keygroups.
In Alpha Setup 2, if you navigate to the Scale and Tonic control mode, then press and hold the 'Scale mode key', you will see three LEDs light up, adjacent to the keys marked '1, 2 and 3' on the diagram. Selecting these modes will then give you the option to configure the scale of the keygroup which corresponds to the number labelling the key on the diagram.
You will then see the generic 'Scale and Tonic controls' view as shown in Diagram C on p12 of you Quick Reference Guide. If you were to press the key labelled '5' on the diagram, you will change the scale of the keygroup number you have previously selected.
This convention is also followed in Alpha Setup 3 - you just have more keygroups that you are able to configure, so more LEDs light up when you press and hold the 'Scale mode key'.
However in Alpha Setup 3, there is also a 'Global Scale and Tonic controls' mode. If you select this, the scale/tonic that you select (you will get the same generic Scale and Tonic control mode' as referred to in Diagram C p12) will be apply across ALL the keygroups (i.e. wherever you play on your Alpha, that scale/tonic will apply).
I hope this is helpful - if you have any more questions please do not hesitate to ask.
Sam
Eigenlabs Software Department