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I suspect you may be unsure about the general principles, rather than the specifics in those places.
The basis of checking in covers customs, immigration control, health, and environmental controls.
Originally a vessel arriving from overseas requested clearance to enter or pratique. This was shown by flying a yellow flag on the port shrouds, anchoring or going to a quarantine berth and was for medical clearance that plague or suchlike was not aboard. Customs and immigration followed once the vessel was found safe.
The yellow flag and pratique still apply.
Advance notice given by by radio is also required often by VHF on entering territorial waters.
However some countries now require 10 days notice by fax or email and a schedule of details eg crew and passport numbers so it pays to check directly with the country's site.
You cannot land other than at an authorised port of entry, for obvious reasons like dropping off drugs or illegal aliens first. Nor can you strictly have physical contact with another craft.
In some places Customs, immigration, and Agricultural people will come to you or you will be told where to berth.
In many only the skipper is allowed ashore to initiate the formalities. He should have the ship's papers and all passports. The fine details vary with the formality of each country. In most all wait aboard.
Clearance out of the prior country is required. One it shows where you came from, and accounts for none of the crew being left behind.
Clearance is not required for a US boat leaving the USA but is required on arrival from a foreign port.
Visas may be required. In the US they are not required for non work visits for people from some countries, but it seems they are if they arrive by private yacht. This is why it pays to check the small print direct.
Conventionally the host country's flag is flown on the starboard shroud above that of one's own country.
It maybe that in the Caribbean because of numbers some less formality may apply, however generally with greater security consciousness and strict regulations it pays to get the formalities right and tug one's forelock.