You can explicitly specify the signature identifier (if they have different names) and the GUID of the initialization profile.
EDIT: CODE_SIGN_IDENTITY[sdk=iphoneos*] = iPhone Developer: John Doe (ABCDEF) and PROVISIONING_PROFILE[sdk=iphoneos*] = provisioning-profile-guid in the configuration (or on the command line). Or, in the project settings, find the “sign” and use the nice GUI menu.
Alternatively, use a different user account for your work builds.
EDIT: System Preferences → Accounts and Add New User. It also helps if you enable fast user switching in the Login Options section.
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