excuse the crap artwork, I just finished a 6-6 Nightshift
the black outline is your case,
the red box is the area covered by your Mobo when its in place,
the grey boxes are holes you cut out of the Mobo tray to allow your cables access
(best position will be figured out by you obv)
the blue box is for your ide cable (Try tucking your sata lead in there too)
and the orange box is for all your psu leads to neatly tuck down the side of your psu and behind the mobo tray before going wherever you need them to,
obviously you will decide on the exact 'best' positions for each cut, and be careful not to snag any cables on pins at the back of your board,
a little insulation tape round the front panel leads to tidy them up a touch
those leads currently taped to the fan will be nicely hidden on the other side of your mobo tray like mine are,
feed the one molex you need round the side of the mobo near the pci slots and feed it to the socket on the mobo,
It takes planning, more planning and thought, but when people ask where your wires are, its all worth it
Moto