Right ho, excuse the shoddy artwork, it is 2am here after all.
The red is where the 24 pin mobo should come out, or I think the hole for the CPU back plate access (That massive one that cuts the motherboard tray almost in half) should extend just beyond the motherboard, in which case thread it through there.
SATA connectors should come through the red hole as well.
The yellow circles indicate the stand offs for the PSU. This means if you flip it so the fan is faced down it can still breathe. It'll also look a lot cleaner as the wires won't be coming across the PSU and you'll see less wires.
Once you've flipped the PSU have the wires leave through the green hole, as you've already done.
Ideally you'd have the CPU power cable coming out of the blue circle but if you can't reach that far then wire it similar to:
After this it should look much better
Also post a shot like the one I've edited, so that we can see the whole case and not have to piece each picture together