I am in the process of drawing a template for my guitar. I have the neck pocket traced in. What is the most accurate way of placing the bridge? Place the neck and go exactly 25.5 inches to the saddle(It is a 25.5 inch scale neck)? Measure from the 12th fret? How much room for error is there?

Also, how deep do I route the neck pocket? I have heard the standard is 5/8 inch. How can I be sure this is right for my guitar?
The string length is never exactly the same as the scale length because you've got to allow for the action. When you press down on the string it makes the note go sharp and out of tune and you have to allow for this. Different bridges have different allowances you need to make. Go here: http://www.stewmac.com/FretCalculator and put your specs in and down the bottom it should tell you the distance to put your bridge.

As for the neck pocket; what sort of guitar is it?
It's a Warmoth neck, and the body will be sort of just a traditional Ibanez shape.
If you mean an RG then usually the depth of the pocket is the thickness of the neck wood minus the fretboard and minus 2mm. This means the fretboard and 2mm of the neck sticks up above the surface of the body and the rest of the neck is below the surface. This should be about .67" in depth. Warmoth does stuff to fender specs and fenders usually have a shallower pocket but there's no problem making it a bit deeper. JEMs are even shallower.