Need Help with Site Structure

I have a web app that is totally reserved for specific customers. Each customer has their own log-in and separate database.

At present each customer is given a sub-domain of the main site (www.customer.mydomain.com). Thus the site file structure is...

public_html
...customer1
......working files
...customer2
......working files

This structure is fine with 2 or 3 customers, but as I get more it will become very tedious keeping all of the sub-directories up to date. There are only two files in the "working files" directories that are unique to each customer (company logo and the configuration info for the database).

What other site structure might I use to make the updating of scripts easier?

TIA for your assistance
jdadwilson