Integrated Webapp saas into wordpress

Hello,

I want to integrate a web application (PHP, SQL) in a SaaS WordPress multisite network setup with subdomains (user1.myapp.com, user2.myapp.com).

The idea is to use only WordPress to manage users and control access to the application (subscription, quota disk space).

The subdomain created by a user is associated with a subdirectory containing customizations SaaS application (cache, themes, uploads, languages).

Each subdomain will allow a user to manage his site directly in its own version of the web application (SaaS setting, account).

Example:

http://website.com –> WP
http://user1.website.com/ –> webapp served rom root/app/users1 subdirectory

root/
	WP/
		index
		registrer
		login
	app/
		application/
					controllers/
					models/
					views/
		content-user/
					user1/
						cache/
						themes/
						uploads/
						langues/
					user2/
					user3/

I thought to integrate my application by creating a WordPress page template, but how to handle road issues (app) and WordPress.

source: http://wordpress.org/support/topic/integrated-existing-web-app-into-wp-not-the-other-way-around

Do you have any tips on how to make the integration of SaaS app in wordpress?

Thank you for your help.

Cordially