A-300 Pro, reprogramming the A1 - A8 Buttons

 I am just wondering how to program the buttons A1-A8 without losing the console controls and transport controls. Last time I tried I lost these controls, so I had to reinstall the A-Pro pluggin for Sonar X1. The reason I want to change the buttons A1-A8 is because I want to use them in the Amplitube 3 plugin to control my effects pedals and I do a live performance. At present I have not had any luck doing so. I have tried using nanoPAD2, to control my effects keys but the plug in doesnt recognise the midi Controller. I have set it up in the Midi Surface Controller but still no luck. I have set Amplitube 3 in both Softsynth (VSTi) and Audio Effects (VST) but no luck. I am told by IKMULTIMEDIA that I should be able to set up midi controls to control use in the Amplitube 3 plug in but no luck. So I am hoping I can use the A-300 Pro buttons A1-A8 to control the pedal effects in the Amplitube 3 plugin for Sonar X1. Can anyone please help me out with this.