Like vristang said be careful when tightening up the waterpump bolts. Use plenty of antisieze on them when you put them back in. If you ever have to change the water pump again you will thank yourself. Getting replacement bolts can be a real pain in the ass.
It is pretty straightforward. I usually just unbolt the accessories and lay them off to the side, i.e. ps pump, alt and a/c compressor. Be careful when taking the water pump bolts out as sometimes they have the tendency to snap off. Should take a few hours if you haven't ever done it before.The most time consuming part is getting all of the crap out of the way so you can actually unbolt the pump.
They will only go together one way, if you consider where the acc. mount up.
If you are worried about it draw a diagram of the w/p, showing each bolt loc. Number each location on the dwg, then number each bolt (piece of tape will work) as you remove them. That may make things much easier.
Best you can do is try to and think through where everything will mount up. I have screwed it up (actually I think I screw up the bolt locations every time I pull the pump or timing cover). As long as you catch the mistake before the silicone cures you can just pull the bolts and move them. I have actually pulled these after the silicone had cured and had no issues.
What kind of silicone should I use? Will the antiseize cause the bolts to losen from vibration after I replace them, like a few months down the road? I plan on marking everything bolt wise as well as use the digital camera as my template.