This isn't something where you can leave out details in how you have set up your relationships between tables and still get help on how to fix this. I suggest a detailed post--perhaps with a screen shot of manage | Database | Relationships where we can see and understand each table occurrence and match field involved.
It will also help to know what version of FileMaker you are using. Execute SQL might be a major problem solver for what you need here, but only if you are using FileMaker 12.
Libraries have the same problems when assigning a new book to Library of Congress. It is easier to assign Top/Down than Bottom/Up.
I would ask how you do it on PAPER? FMP can be incoded to follow your paper steps.
I would think assigning a Table to each Layer of hierachies and each Table assigning its own Unique Serial Number would lead you to then bottom of the list [Objects]
Thus and object will have "Assignment" ID for each Layer...
So i would create an Object layer by top/down and then decide to NOT enter the structure Name after the creation of a new object layer Top/Down.