If it were me, I'd fill the empty tank with RO/DI, and add salt to get the salinity correct, unless you're buying SW? You could then put the rock in, although I've always like to get the substrate in first, then add the water with a big plate on the bottom, to keep it from stirring up the sand too much and clouding the water. Lots of ways to do it though.
I had this exact same issue when I bought my 130D. However, Pinky ended up sending me a new lid over the skimmer bay that has the ribs shaved down. It still doesnt sit 100% perfect, but it is much better. Another thing to look at/adjust are the white plastic hood pins. If you rotate them 90 degrees or so, it should realign the skimmer hood and timer flap so they sit flush. Every time I raise tank hood to its fullest upright position, I have to readjust the white plastic hinges. Here is the link to the problem I was having. http://www.reefsanctuary.com/forums/red-sea-max-owners-club/43220-joining-club-3.htmlI did have a couple questions though:
1) The hood part that goes over the skimmer does not shut down flush like it should. I have checked and double checked the skimmer was sitting properly but still it won't sit flush. Same goes for the cover over the light timer.