The control codes that the app sends to the Arduino are not dependent on the actual pins used. The pin definitions are only used inside the sketch. This means you can move the pins around without changing the apps.
In V3 I have moves many of the connections. All the solenoid pins are now on the same register which will allow easier direct pin addressing in the future.
The new connections also take in to account a slightly different layout when using protoboard.
I should note that I have changed some of the control codes so if you are using the new apps with an older sketch not everything will work.