hi slip, 

there is no 'right answer'.  you get to do it any way you want.  i usually use a process something like below:

i will find some layouts on other kayaks that i like and take some pictures and notes and/or measurements as 'inspirations'

next, i will also think about specific things i want the rigging to handle - things like hold a water bottle, keep a spare paddle on board, support an assisted paddle float rescue -- and i will begin to layout the ideas with blue tape testing it with the size of water-bottle, paddle etc against the proposed design.

finally, i will make adjustments for construction and things like avoiding bulkheads or clearance needed for the fitting and the side of the boat. (e.g., if your fitting puts screws through the deck, will you be able to reach the other side of the screw and get a bolt on it?) 

below is an example of 'laying it out' with blue tape.

and after that is the final result:

also here is a picture of my shearwater....same process:

i hope that helps

h