Some in the boat, some out
I keep the following on the top of the boat under the bungies (either in front or behind the cockpit). I keep everything low to the boat so that nothing sticks up higher than the hand pump.
Hand pump under front bungees. I’ve tried other locations and found this works best. I keep it low to the right side of the boat because I do most of my re-entries from that side and it is easy to access, use, and replace. I keep it to the side as that leaves the front bungees free for lower profile gear.
Paddle float under front bungees in front of cockpit. I also keep a spare behind my seat.
Rope/throw rope under rear bungees, strapped down and coiled nicely. I ensure that nothing is loose back there.
Small safety items (whistle, signalling equipment, any safety electronics, water, and light are on my PFD or person. All tightly contained. Larger such devices are in a dry back behind my seat taking up all remaining space and clipped in the boat so that they won’t float away in a capsize.
Spare flares in pouch under front bungees.
Dive flashlight behind seat. Never used it for safety, but if you need a bright light, you won’t find a better, more compact flashlight anywhere.
Spare rope behind seat along with spare float. Yes, I’ve been called Sam Gangee by more than one person.
Spare paddle beneath the rear straps/bungees.
Float bags fore and aft (if one must abandon the boat, don’t forget to extract these - they can be a lifesaver - literally). I carry these even if there is no room to inflate them. Deflated, they take up almost no space and can be used to fill any places that open up as gear (food, mainly) is depleted over time.
I’ve used almost none of this stuff (other than the rope), but when it comes to loading/unloading, it is pretty easy to put it where it belongs and find it when I need it. It is always best to have a set location for safety equipment because if you need it, you need it quickly and don’t want to be fumbling around through a mess of gear to find it.
Also, in cold water, the additional burden of trying to recall where something is could well be sufficient for hypothermia to progress to the point where physical/mental skills are dangerously compromised. Put it where it belongs, keep it there, and you reach the point where you access these items without having to thing about where they are.
Exceptions cause problems. Avoid them, if possible.