That's the normal behavior - built in applications tend to be listed right up at the top, with everything you install listed somewhat alphabetically under that.

To modify the list, click on any icon of interest and hold - after a few seconds it will allow you to move it wherever you want to.

Catorise is a nice addition - it stores everything in category folders for you - it does a pretty good job of this on its own but you can install an application that allows you to customize the layout.