What exactly are you trying to customize?
Look and feel? Hack and play around with the css/html of one of the fusion templates
Functionality? Create your own InvokeURL and InvokeScript widgets, and add them into your Flexible Layout
Have you ever checked this DevTV on Infrastructure Map Server developer center?
DevTV: MapGuide Fusion Technology Introduction
A self-paced video tutorial on how to build a web-based mapping application using the Fusion Viewer Technology and MapGuide Enterprise.
View Online | Download