Typically you would group related layers together that is, if your header graphic or section in the mockup is made up of several elements you would then group these elements into related layers which then are then grouped into a named folder.
this way a developer is working on say your header navigation can look at your PSD file, find the group/folder called header then inside that find the layer(s) called navigation and extract what he/she needs
A lot of developers can do psd to wp (wordpress) ifs not overly difficult, however, I would advise at looking at the available options out their as for me personally wordpress is not one size fits all solution most of the time.
Also, its worth noting the developer may not notice a subtle gradient on layer 166 which is should be but is not found layer sequence 29-34 (example) and such sometimes the outcome is a design that is missing parts, be keeping related stuff together keeps everyone happy.