I wouldn't take the approach of moving all data  from file  servers to SharePoint
for the sole purpose of being independent of file server storage. The reason is
that that approach smacks of lack of Information Architecture understanding and
will cause issues later. BUT== you did and are so, that is a moot point.

The data files  you move can be put in a document library and indexed as long as
the file type is not forbidden. Make sure that the file type is allowed. The
size is also important; make sure that the individual file sizes are small
enough and that you don't go over quota.

The process of using the data  files and the process of storing them are
different, Harold described how to store them, But if you are wanting to use
them in Quickbooks sharepoint  has a check-in and check out feature that you
could use with the document library but this limits you to only allowing one
user at a time to edit the data, I know some companies have multiple users that
use Quickbooks at the same time so this feature could be a plus or minus.