The "Tables" are the list of the tables that are actually IN the file. The Relationship Graph on the other hand can have instances from ANY FileMaker file that you can point to. The Table Occurrences (TO) on the graph are more like "aliases" to the tables; the files/tables themselves do not need to actually be IN the current file itself; it's an abstraction.
It sounds to me as if you created multiple files, of one table each, when you converted some other kind of files to FileMaker format.
If you want them to actually BE IN one file, you need to Import each other file's tables, one at a time, using the option to "Create New Table", as the Target of the Import. This option is at the bottom of the drop-down Target list.
Then they will appear in the Tables, and can be renamed, and put onto the Relationship Graph. Or, if you've already put TOs targeting the external tables on the graph, you can just repoint them to the now internal tables. Likely the fields will still line up, but you should check that.
Excellent explanation. None of the books, not the File Maker Support tools, and not the File Maker Help file gave me a clue. Now I can go forward. Thanks so much!