The protocol book starts its life as a set of pages a notary (a notary must be a lawyer) buys from the government. This is where the lawyer records official documents. Once the lawyer has used up the pages, they must be turned in to get the next set. That's the easy part of the explanation, How and why they are used is more difficult.
These protocol books become the authoritative copy of transactions. For example, if you sell your car, you go to a lawyer with the buyer and the lawyer writes up the transaction. It will contain identification information for the property being transfered and of the buyer and seller. In the case of real property, it is also recorded in the Alcadia but, what is recorded there is ownership--not the transaction.
These books are bound and stored in a vault in the court system in Managua. Generally, they will never see the light of day. The exception is when there is a dispute. The dispute is resolved by locating the legal record (each protocol book page has a unique number).
This is exactly the same system that is used in Costa Rica. At first it seems rather strange. But, the point is that a notary is not a glorified clerk like in the U.S. Becoming a notary essentially makes you an officer of the courts. These documents are then official legal documents rather than random scribbling of the the typical U.S. lawyer which is usually in the form of a threat to some other person.
The catch for us foreigners is that any "notario" transaction must be entered in the book. And, as Spanish is the official language in Nicaragua, the entry must be in Spanish. Thus, the casual "let's get this notarized" we say in the U.S. has a very different meaning here. I did, however, find the way around this when I was in Costa Rica. It just takes, well, the words of a lawyer to come up with the right solution.
If you are asked to "get a document certified" the person is asking you to have a notary certify that this document is authentic. That's all. So, you go to a notary (satisfies who you are going to) and ask them, as a lawyer, to certify the authenticity of the document. So, they write/type on the document that they certify that it is an authentic copy, sign and stamp with their "lawyer stamp". Their signature, of course, included that they were a lawyer and notary. I had one lawyer in Costa Rica add a timbre (fiscal stamp sorta like a postage stamp) because she thought it looked more official.
In any case, you now know what a protocol book, what has to go into it and how to get something very common done "the easy way".