well im using a centralised directory for CSS files and images etc, and customising the templates in WHMCS and joomla. i've included the single css file in both, and just reference each image in the root folder where teh images are stored.
for the menu ive created a php file and have to manually change this, but this gets included in each of the headers on both the WHMCs and joomla templates. basically two sepereate systesm, in seperate folders, but it looks like the same system.
use 'jumi' php module in joomla so i can include the php files in articles. have used it to create forms for login and domain lookups. havent been able to get a client login working in joomla, so i dont display this on the joomla pages. WHMCS controls the client login and management. using joomla articles for content that changes regularily, and have to manually link to products.
using php ive pulled prices from the whmcs database for particular products, and display them on the joomla pages, using the "jumi" module.
using html modules in joomla, i can display and hide content on joomla articles. hve customised every tpl file and used CSS classes from the shared css file to style them.