Multiple domain under same application.

[eluser]gops[/eluser]
I have created one to-do list like application for specific industry.
How do i make different domain to use same application but different database (or different prefix on same database...).

i.e.

www.one.com is todo list for one company.
www.two.com is todo list for two company.

the code is same for both the company but the database is different.

Do I need to make separate folder for each application ? (that will make upgrade hard in case of bugs).

My currrent hosting provider is giving me different folder for each domain (bluehost.com).

Thanks.