sharepoint file-to-file or metadata

My company is moving every department's data to Sharepoint servers.
Currently, our creative department has been using an Apple file server, which is getting old and needs to be replaced anyway. However, in moving to Sharepoint our IT department needs us to make a decision to go file-to-file transfer, or to use the metadata method for moving and storing our files.  We have more than a decade's worth of work in a very well-structured folder/job number system.

My questions relate to which would be the way we should go? Does the metadata method get iin the way of using Adobe Creative Cloud apps, like InDesign and After Effects properly, according to the way they create their work files, etc.?  How are we going to keep linked files stored on Sharepoint linked to their respective layouts?

Thanks for your input!