Included is the COAS manual: Age_of_Pirates2_-_City_of_Abandoned_Ships-UK_Manual_-PC.pdf
Page 24 describes what is needed on the ship for your crew: Food, Medicine, Rum, Weapons
Below is a screenshot where ERAS shows how many days you have of Food/Rum in the upper right, and you can also see items held in the ship's hold. Press F2, click 'Ship' at the top to see a list of your squadron and make sure each ship has enough Food and Rum for the amount of each ship's crew. Also make sure there are some Medicine for each and also the count of Weapons should be at least the number of crew on each ship, in case you get boarded. If there are not enough weapons, then the crew without a weapon will instantly die in a boarding action; with weapons, then their experience and numbers will help you fend off boarding attacks better.