For me, manuals are kept in (several) separate binders from that which is my boat document binder.
My boat document binder has:
Section 1
The original boat registration document, and several copies.
FCC Licenses(which also documents MMSI), Ship Station, my operator
permit, and HAM.
EPIRB registrations.
Liferaft inspection/certification.
Current crew list, with
emergency contact information, and several copies.
List of previous
ports, and several copies.
List of significant equipment, and several copies.
Section 2
Any relevant
medical information, Vaccine records, prescriptions etc, of the crew.
Section 3
All paperwork provided to me from my last port of call (under passage)
or my
current port (while in port)
Section 4
All paperwork from previous
ports of call.
I have copies of many of the documents in the binder for convenience. It is appreciated when asked to see my documentation for example, if I give them a copy and tell them they can keep it. Some officials will sign and stamp my crew list instead of filling out another couple pages of forms. Else, it makes it much easier to fill out the forms with the information all in front of you. And
customs in many countries wants a list of equipment on the boat, etc. It makes the process much faster, and reduces the number of questions, which always seems a good thing.
Especially when there is a language barrier. Checking into
Indonesia, without an agent, I simply gave the officials all the papers I knew they would need(and some they didn't) They had no questions for me, they just filled out a bunch of forms, typed on the computer, and then we each stamped everything.