Yeah, most of the wires are behind the motherboard and underneath a black plexi custom cut panel on the floor of the case the same one you see on the side of the bay section.
As for having all those wires being safe behind the motherboard, it is at least for me cause I put a plastic sheet on the back and it helps that the standoffs on this case is 1/2" tall.
Right now my poor little winnie 3500+ is at 2420Mhz/220x11/2-2-2-5-2T that pretty much all I can squeeze from her. I went H20 for quiet computing, I really hate those loud fans after a while.
Overall I just wanted a clean sleek looking rig and of course quiet. Below is a list of my specs and my soon to be upgrades.
MSI K8N NEO4 Platinum (Updating to a DFI Lanparty UT RDX200 CF-DR CrossFire)
AMD Athlon 64 3500+ 939 (Updating to a AMD Athlon 64 X2 4400+ Dual-Core or a 170 Opty)
Crucial Ballistic Tracer, PC4000 2GB DDR500 (Updating to 4GB Corsair 3500LLPRO, 4pcs 1GB)
ATI Radeon X850XT PLATINUM EDITION (Updating to a ATI Radeon X1900 XTX 512MB)
Creative Labs X-Fi Sound Card
Seagate Barracuda 160 GB7200.9 RPM SATA3G
Seagate Barracuda 500 GB 7200 RPM SATA3G
Plextor PX-716AL Slot-Loading Drive
Sunbeam 4 Channel Rheobus
PCPower&Cooling TurboCool 510 PCI-E PSU (Modded)
SilverStone Black Temjin SST-TJ03 Aluminum Case
Windows XP Pro/XP Pro X64 Dual Boot
Danger Den TDX A64 Copper 1/2" ID Water Block
Danger Den Maze4 Chrome Water Block
Danger Den Black Ice Xtreme II Dual 120mm Chrome Radiator
Laing D4 12v DC Pump, PolarFLO Machines Chrome Pump Housing
PrimoFlex 1/2" ID PVC Clear Tubing
4x Evercool 120mm 4 Blue LED Aluminum Fan
2x Evercool 80mm Aluminum Fan
Danger Den 1/2" Chrome Fillport
2x NorthWater Xtreme Water 6" Chrome Xchanger