The instructions that you are referring to are likely predicated on whether or not you want to use CCP based installer as the delivery system. You do have a choice here on which installer delivery you want to use. It will either be the CCP installer or going with the Acrobat MSI installer. So, first make that decision and then the instructions might make more sense.
Q1: Personalization -> a. In this scenario (am a CCE customer, configuring a package to be deployed via SCCM) what should I do with "Allow standalone Acrobat deployment with CCE serial"?
Response:
A. If you are using CCP installer delivery you don't need to apply the serial number here in the Adobe Customization Wizard DC.
B. If you decide not to use the CCP installer and decide to go with simply using the Acrobat MSI installer using the Adobe Customization Wizard DC, then put in the CC serial number in the SN field and push the Get Offline Exception button. Note, you need to be on a machine that has internet access to do this procedure.
Q2: Open SCCM > Software Library > Create Application -> a. Windows Installer (some things say to use the installer, other things say to use the MSI. Please explain!)
Response: Again, it depends on the choice that you have made on whether or not to use CCP or the base Acrobat MSI installer. If you are using the base Acrobat MSI installer then it's not that different than what you are used to doing with any other MSI based installer.