I personally use a custom / other script for my billing and ordering. Maybe you have herd of it - NeoManager / WHManager. It's a freely available script - but we have had it modified to suit our company the best it can.
To test out this script you can see it in action at www.avidnewmedia.com
. It's pretty slick for the price (free).
One thing which we have found extensively difficult however is making the administrator interface based around templating, to try and alter the look and integrate it into our website. It appears that the HTML code is embedded into the PHP code, which makes it hard to edit.
Definitley a good pick though, either that or ModernBill!