It will only recognise the links table when adding/verifying as it is reading from the Links def file so you can add columns to the Links table and the admin panel will pick it up, but with a seperate table, Links SQL won't recognise it by default.

Alex may be able to prove me wrong but the only way I can think is to create a seperate script that would list your links and have a multi-select, again with the links listed allowing you to select a link and then select related links for the link you selected and then insert it into the new table. (if that made sense )