The mag 3 shown in the location above the main tank is a problem. In that location these kind of pumps can not self prime, would be difficult to start and can't restart if the power fails. You must place the pump below tank level.
I would avoid the connecting tube for the reasons outlined by ChuckG. In addition to the cost, it's going to be rather small, and few fish will be interested is swimming through it. Also it will be extremely difficult to clean.
If you are going to have two tanks set them up with a common filtration system, or set them up as two systems. There are advantages either way. You might find it easier to put the tanks more or less side by side and put the door to one side or the other. You could also consider one larger tank, which might be the least expensive option.
One other thing the refugums above the 90 gal tanks will be very difficult to work on. You'd be better off in a side by side configuration. You need about 12 - 18 inched over a ank to work on it at all, and by the time you add it all up the refugiums top frame will be 7 to 8 feet off the ground. You'll need a ladder just to get to the tank, and that's risky.
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