In light of recent posting about removal of the flotation blocks.....make darn sure you either label the blocks or mark them so they go back to the same location the factory installed them....they are wedged into location....friction fit.
For my 2013 PA-14 I used Scotty flush mounts for my down rigger and rod holders.
I am right handed, so the mounts are mounted to the mounting boards on the left side of my PA.
Both flush mounts are inset 1/4" from the right edge of the mounting board....this allows use of fender washers on the outer machine screws and there is still enough room to secure the locking nyl-nuts on the inside edge or vertical wall of the kayak.
The center of the hole for the rod holder is 4 1/2" from the bottom edge of the mounting board and the center hole of the rod holder is 11 1/2" from the bottom edge of the board....there is enough room/separation between the rod holder and down rigger to my liking.
I like this spacing as I can easily work the manual down rigger and grab my rod out of the Scotty power lock rod holder.
Lastly, like any project that requires drilling or cutting......do a dry run layout to be sure you like the location, then measure twice...