I think that this may be a re-occurring theme here, but here we go with a "I screwed this up, hope you don't".
You need to really think through your setup for checkin/checkout for SourceSafe files especially when using VSTS (Especially if this is your first time using VSTS). I really didn't get the best direction when setting mine up, and used a basic "Work" directory for my initial checkout, made some changes, and checked them back in. When I had to work on another branch for a hotfix item, I wanted that segmented out, so I created a sub folder in that same directory, pulled files down, and started to work. But when I had to go back into the original code to demo it, I found that when I tried to "get latest version" it started looking at the second branch as a new sub folder of the original (ie. it became a nested project). Messy situation, ended up discarding all changes and blowing it all away.
The nugget of wisdom that I have is that when you are looking at your Source Control Explorer there is a "Workspace" dropdown that will allow you to select your local file setup and modify it. You need to select workspaces from the dropdown, and click edit from the items listed.