I'm going to install multi-org functionality for my MC account. At first I should install a connector itself (version 5.494 or higher) and then log a support ticket in the Salesforce Help and Training portal to complete the upgrade. The question is - what about API user and Salesforce System user? Should I proceed with standard configuration for non-multi-org first? Or are they a completely different process'?
The api user is required for the connector to work. It is what allows the connector to access records. If you have not already done so, I highly recommend getting Premiere Plus support at least through the setup phase.
The order in the documentation is a bit confusing, it says before upgrading to multi-org, review that you have Enterprise 2.0 Marketing Cloud account with multi-org is enabled.
The documentation also assumes you have a connection with Sales Cloud already established.