Like any good long term relationship, start slowly. I recommend that you take your kayak out on the water several times naked. No, YOU should wear clothes....or at least your PFD...but don't go crazy rigging up your kayak and tossing four or five rods into your crate for the maiden voyage. First off, no matter how much experience you have, there will still be differences in the feel of each brand and model of kayak. You want to make sure that you are comfortable in the way your new kayak handles before you start loading it up with gear. Why you ask? Well, if you turtle your new kayak loaded up with gear, you now have two issues. Issue one, getting back into a kayak that you are not 100% familiar with. Issue two, unless that gear is secured, you are now fishing for gear, not fishing for, well...fish.
Another important aspect to remember is that if you start drilling holes for gear track, anchor trolleys, and other accessories, those holes will be there even if you decide that the gear isn't set up exactly where you want it. While there are ways to fix small holes in your kayak, most people prefer not to do repairs on their brand new hull if at all possible. There will be plenty of time for rigging gear. While there are quite a few "must have" items found on almost all fishing kayaks, rod holders, and storage crates come to mind, their placement can be highly individualized. Take myself for example. Had I followed the internet recipes for rigging my kayak, everything would have been backwards for me since I am left-handed.
To wrap this all up, kayak fishing is a great sport and a wonderful way to spend time out on the water relaxing. Relaxing is the key word here so no need to add any stress when you break the champagne bottle on the hull and head out on your maiden voyage. Take it slow, learn your kayak, and have a great time!