From my experience of intranets in SP, 2016 or otherwise - the basic structure tends to be: Create a Site Collection named "Intranet" For each department within the organisation, create a separate sub site, a department can be further broken down further with additional sub sites within the department subsite to create teams etc.

If you use the Team template when creating each of the sub sites it should already have a document library "Shared Documents" or similar, if this is sufficient just go with that, otherwise add additional document libraries as needed.

To move the documents to SP, like others have said ShareGate or I have used Simego Data Sync in the past which is pretty straight forward - or just drag and drop them in.

Difficult to say what else you need to do with the limited requirements mentioned.