Hi Jack,
If you intend to customise the background yourself you should download any of these templates and modify them in something like photoshop -
picasaweb.google.com/millidge/MicroPuttGAMEImageTemplates#
It all depends on whether you want a coloured background or on white or black etc.
If you want a colour to match your website, pick one of the colour templates and adjust the hue in photoshop, its quite a quick way of changing it to any colour you like. Then copy, paste and skew your logos onto the model.
Regarding the clicking issue, the only restriction I'm aware of is that you can't click outside the game window, as with any flash movie.
Good luck!
Reece