You have several choices:
(1) Email your IPA files to employees with install instructions into the desktop iTunes App.
(2) Create your own web server, put your IPA files up on the server. Provide instructions for iTunes app installation.
(3) Use a product that provides over the air distribution and helps in deployment and management, handles updates, reports on downloads, etc.
If option (3) makes sense, look at EASE (Enterprise App Services Environment) from Apperian which is specifically designed to help developers deploy and manage apps in the IOS environment. The program is free for developers using ad-hoc profiles, you can sign up at http://www.apperian.com/ease.
Note that you will have to join the Apple iOS Developer Enterprise Program (IDEP) in order to build "enterprise" apps, but this is easy to do now that Apple has lifted the 500-employee restriction.
