Each "flag" locator MUST have "penn" locators as well. So basically on each mast, you would have equal numbers of flag and penn locators in total on your ship.
Then you can select what you want in ships_init.c . Sometimes what you set doesn't correspond with what you get, so it can be a bit of trial-and-error.
If you make subsequent changes to ships_init.c, you need to Reinitialize (F11) and re-give your ship to you with the console (let me know if you're unfamiliar with that).
Otherwise, starting a new game will make it work too.
Then you can select what you want in ships_init.c . Sometimes what you set doesn't correspond with what you get, so it can be a bit of trial-and-error.
If you make subsequent changes to ships_init.c, you need to Reinitialize (F11) and re-give your ship to you with the console (let me know if you're unfamiliar with that).
Otherwise, starting a new game will make it work too.