howdy and welcome to the site.. :D
it will work but I wouldnt drill both tanks if you dont have to.. if you can I would raise one tank higher drill it and run the tube over the top of the other.. I have a similar design as yours but I split the main coming down one line runs to the refugium the other line runs to the sump.. I like it that way so I can control the flow going into the refugium using a ball valve...then the refugium dumps into the sump..