Just think about what you need to connect up.
At the top middle of the board you may need to run fan cables down and behind the board towards a fan controller and also the 8 pin CPU connector.
Unless you have something to connect to I don't see much point in the top right hole you have.
Right side middle you have the 24 pin ATX connector.
Right side lower you have the graphics card power....
....and below that again you have your SATA connectors which will
At the bottom of your board you will have the front panel connectors.
Most cases will have one or two largeish holes at the right hand side, around the periphery of the board, one or two holes or a longer slot up top and then maybe a nice slot just next to the PSU.
Have a look at internal pictures of cases like HAF X, Corsair 600D, Antec 1200. Basically any modern non-dirt-cheap case for ideas on where to put them.
Some U channel run around the holes would make the holes look a lot better too.