In all three of the boats we have owned, we have "discovered" our own personal choices for where things "need" to go. Our most important criteria has been: quiet. This means NOTHING makes any noise, at the dock, at anchor, or underway. Accordingly, only YOU can find the answer to the proverbial "A place for everything, and everything in its place." As you begin to "occupy" your boat, you will find what works for you best.
For example: I've known hundreds of folks with the same boat we do (and been on most of them, being active in local fleet when we lived in SF and visiting many across the country as secretary of our association) , and just about everyone has found a different place for, of all things, their paper towels! Our installation, done by the PO, was to cleverly place the holder under the top companionway stair tread. Others have placed them in the galley with holders right on the strip between the forward part of the galley counter above the settee seat-back. Yes, it's maybe closer to hand, but, to us, it breaks up the open space, and we think it's "wrong" because it makes the space feel smaller from the visual "intrusion." I just grab a paper towel before I get my hands wet, assuming I remember.
While it's an outrageous example, I think it's applicable to just about everything. There simply isn't a "right place" for things, only you can determine what's right for you.
Deep lockers are something else, but I don't think we could answer that until we know what you plan to or need to put in there. There's a difference between storing your dinghy motor, or just boat hooks, brooms and winch handles. Many folks have found that layering and buckets work. Others have built shelving inside the caves.
Open cabin shelves are a particular challenge. But here, too, what you want to put there has to come first. Books can be accommodated by building removable fiddles or even shock cord, and sometimes depend on the size of the books. Edge fiddles can keep other stuff in place. Lighter stuff should go higher, for obvious reasons.
Congratulations on your new boat. Have fun making it yours.
