SharePoint Migration Tool - How To Migrate a Folder and Subfolders

I have to migrate over 100Gb of data into SharePoint.  There are 20 folders that I need to migrate into a document library yet maintain the existing folder structure.  When I migrate one folder from our file server, it copies them into the root of the document library instead of taking the main folder and copying it along with their subfolders. 

Is there anyway to have the tool copy the folder I'm selecting and copy it with its subfolders versus just copying the subfolders of the folder I've chosen?

If I migrate the folder then try and select them all and "Move To" another folder, I run into major issues with it deleting subfolders during the move as many of the subfolders have the same folder names.  It's a mess.

We must maintain our folder structures.

I can't simply copy the folders to the site using a browser and many of the features of the tool get ignored (ie it fails on any file with a ~ in it, fails if folder names are too long etc) and there is NO quick an easy list of the failures.  The tool allows all of these to migrate.