So I think there are a few questions you must first answer for yourself before attaching anything to your yak.
1) The main use of the kayak. i.e. what type of gear do you need to carry and use to catch the intended species your will mainly be pursuing. How are you using that gear? i.e. will you be trolling, using artificial baits, Live bait, ect. This will dictate what type of accessories and the placement of them.
2) What is your budget? This one factor will dictate what type of gear and accessories you will be adding. The big thing here is that you may need to buy one item at a time and you need to decide which item will have the highest priority in installation and use.
The things I am going to discuss are only suggestions and what has worked for me, so keep that in mind that these recommendations are just that, "suggestions" with room for you to make decisions and and find what will be best for you. The best advise I can give first and foremost is to fish in your yak first then decide over time the best placement for anything you intend to use.
Some materials I use for mounting stuff-
Lexel sealant- can be bought in the paint section of most hardware stores. This is similar to Silicone sealant, however it dries slower, bonds better and is a little firmer than silicone once cured.
Stainless steel loc-nuts, bolts and washers.
Tri-grip rivets or load spreading rivets- these you may need to order from any kayak supply store. have found that the rivets you get from the hardware stores do not work as well as these do.
Trolling: this method is used when you are using live or artificial bait. basically you play out line behind your yak and move forward pulling your bait behind you at a steady pace. If you plan on using this technique you will need some sort of holder to hold your rods while you paddle. I prefer these rod holders to be situated behind me within easy reach.
Most fishing sit on top's usually have flush mount rod holders installed, but if yours does not, it is very easy and cheap to mount a pair of them. other options include rocket launcher type of rod holders like the ones made by Scotty and RAM. Note: if you plan on installing a flush mount rod holder make sure that you purchase the type that are sealed and will not allow water to enter the inside of your kayak.