Regarding this construction of yours, "It includes a 3,000-tonne supply ship and a patrol vessel, all of which will spend the next five to 10 days fishing in the area," the use of "all" is incorrect because only two vessels are involved; "both" should be used instead, as follows:
"It includes a 3,000-tonne supply ship and a patrol vessel, both of which will spend the next five to 10 days fishing in the area,"
We should also keep in mind that the above construction would be correct only if the statement preceding this sentence makes it clear that the other vessels in the flotilla would not be involved in the fishing activity. Otherwise, the indefinite pronoun "it" has to be replaced by "all of the vessels" and the sentence needs to reconstructed as follows:
"All of the vessels, including a 3,000-tonne supply ship and a patrol vessel, will spend the next five to 10 days fishing in the area."
When linking coordinate clauses, the general rule is to put a comma before the second coordinate clause, as in "My fiancee lied to me that time, but I took her word in good faith." But when both coordinate clauses are short and simple, the comma can usually be dispensed with, as in "She lied but I believed her."