Hi Bill,
If your AIP project generate also an MSI and an EXE file it means that in the Builds page its type is set to "EXE setup with resources next to it".
In this case you can set also the MSI name and the EXE name for you output package.
For example if you have an "EXE setup with resources next to it" package type and you set the MSI name "MSIfile" and the EXE name "EXEfile" in the output folder you will find an exe file called "EXEfile.exe" and an msi file called "MSIfile.msi".
If you have a "Single EXE setup (resources inside)" package type and you set the MSI name "MSIfile" and the EXE name "EXEfile" in the output folder you will find only an exe file called "EXEfile.exe", but at the install time the MSI package is extracted from EXE in the "Extract Location" where it will be called "MSIfile.msi".
In the
Difference Between MSI and EXE article you can find some differences between MSI and EXE.
Let us know if it helped, otherwise give us more details about your scenario.
Best regards,
Eusebiu