There are a lot of guides showing different cable management techniques, but none of them are a substitute for experience. When you've done enough of them you develop an instinct for it which is hard to put into words.
Here is what I would recommend:
1) Write down everything that is connected so you make sure you get it all connected again afterward.
2) Disconnect everything.
3) Starting with the biggest cable and working down to the smaller ones, attach them one by one, routing the cables out of the way and away from fan blades, etc.
4) For now, use twist ties to wrap up each individual cable as you attach them, again - one at a time.
5) When you are done and everything is connected, look at the whole works with a critical eye and look for ways you could have done things better. (That's why we stick with the twist ties for now.)
6) When you get to a point where you think you've got it as good as it's going to get, replace the twist ties with cable ties. Pull them snug and clip the ends short.