Xpadder is a macro program. In other words it maps keyboard commands to your gamepad. So if you want button one to be the 'A' button for no$gba thenyou must map the keyboard button that you use for 'A' in no$gba to button one using Xpadder.
Just as an example of it's versatility: if you use VBA you can even set it up to savestate your game for you (by mapping Shift+F1 through to F10 to a single button which it will each cycle through saving on the next savestate every time you press the button (so if you saved on State 1 last then the next time you press the button it will save on State 2, then 3 etc.) and you can do the same for loading of the states.