Check, double check and triple check each connector is connected correctly and to the correct point before switching on!
And normally I would run the machine the first time with the case off, just to check all the various fans etc are working correctly.
If possible find a little nook where unused connectors can be tucked away.
Finally. I try and hide as much witiring as possible behind the mobo. This usually requires some thought and planning, and taking out a screw or two from the corners so I can thread the wires through (then re-inserting the screw of course!). This keeps the path between the intake and exhaust fans as clear as possible reducing heat build up, and makes the internals easier to work on.