Whenever you check out a database object, Team Coding will check to see if it exists within the VCS provider. If it does not, it will add it to the VCS provider the first time. It sounds like your Team Coding configuration is not matching your existing Subversion setup. Team Coding is very flexible on its configuration, and there are a number of ways you can try to get the Team Coding configuration to match your existing Subversion structure; however, it would help to know what that structure is.
You don’t need to use a flat-folder structure if you don’t want to. Team Coding is very capable of creating a custom folder structure for your objects. For a guide on setting up and configuring Team Coding, you can reference the following ToadWorld blog article (“Getting Started with Team Coding (NEW for Toad for Oracle 2016)”), which has a PDF document that outlines each step. Of course, if you have any questions on how to set up a specific custom setup, please feel free to post the question on here with what structure you’re trying to create, and we’ll do what we can to help. The getting started guide is located here:
I hope this information helps. Please feel free to let us know if you have any other questions, or if there’s anything else we can do.