Hi,
They do have different purposes. There should always only be one script in the Install folder, and all subsequent scripts should go in the upgrade folder. The version of the script is recorded in the database so we never run scripts that have already completed, so we can re-use version numbers in the upgrade scripts folder.
Now the purpose of the install folder being separate instead of just putting all the scripts in one place, is because over time the number of scripts keeps growing and we get to a point where we don't want to run every script that ever existed for new installations. Even now, the number of scripts run for mojoportal-core on a new install is pretty long and soon I may create a new install script that consolidates the current schema into one higher version script so that new installs don't need to run so many. So with a newer version install script it would just skip over most of the upgrade scripts since they would be lower versions, but those upgrading from older versions won't have any missing scripts in the upgrade folder even if they haven't upgraded in a long time.
Hope that explains it.
Best,
Joe