How to: Multiple iOS Enterprise Applications inhouse
Are you using two different bundle IDs in Xcode's project target?  That's the string that looks like this:

com.yourcompany.app1
com.yourcompany.app2

or

com.yourcompany.allapss.app1
com.yourcompany.allapss.app2

If I assume that you've done your provisioning profiles correctly, then the reason an app would replace another would be if they had identical bundle IDs.