Sounds like you're new to kayaking. You start to learn through experience (what you carry) that works for you. I like four holes with a square and (X) in the center. I carry a water bottle in the summer and in winter a dry bag with a hood and extra gloves etc. The (X) in the center is what works best for me. Most American kayaks use that. If I have to help someone, I can slide a paddle under there easily to get it out of the way. The British kayaks seem to use the three bungees across the deck. I carry a spare paddle (Greenland Storm) so I have two loops on the back deck. Lots of paddlers carry a spare paddle. Those loops for a paddle float re-entry work well and I have put them on past boats but now I'll leave them off since I'll do a re-entry and roll if I'm ever swimming and can do a paddle float entry easily without them. The most important thing is the group thats in front of you and what you think you'll possible carry. One thng I learned by mistake is to not have that group in front of you too close because it can interfere wih your paddle stroke.

You can always add others later. You'll be able to reach up from you hatches forward or back for access. (depending on what kind of hold-downs you planning on using) If you're doing recess fittings, yes, you'll probably want to do it now.

Lots of kayakers use deck lines. Lines that run from the front of the bungees to about 2 feet shy of the bow and back on the other side. They are for the day you are crossing tha North Sea and find yourself in the water and need to grab something quick so you don't get seperated from the boat. The british boats really like those things since they seem to get carried away with the dramatics.
In the beginning, hopefully you'll paddle safe and conserative and never find yourself in the water. Check out some commercial boats for ideas. I don't think any builder wants to muck up their boat with too much junk.