You should use the standard upgrade procedure whenever possible to ensure you have the latest features and fixes. Only use the custom upgrade when you have a specific reason for installing an older version.
With OnApp you can upgrade to a custom CP version, i.e. not the latest one available in production. Make sure to update within the same major version. For example, you can upgrade from 3.2.2-9 to 3.2.2-x, but not from 3.0.x-x to 3.2.x-x.
To upgrade to the specific OnApp Control Panel version, perform the following steps:
Run the following command to eliminate all of the files which yum uses to determine the remote availability of packages: