As Chris said really it is up to you. The reality is that the state of a deck would have changed significantly depending on the circumstances (are they cleared for action or just sailing along). So you have essentially two choices:
Pick the exact scenario you are trying to depict and do so accurately (e.g. show the tackles laid out if the ship was ready for action or shut the ports and secure the cannons to the side of the bulwarks if just sailing along).
Do some sort of representative scenario (this is what most people are trying to do). Essentially you are depicting some of the many things that were done on the ship even though it is technically inaccurate to have them happening simultaneously. But in this case it comes down to what you want to depict and how aesthetically you want to present it (a ship model is a work of art after all).
Though with #1 there might be a technical right answer there is most definitely no right answer to number two as it depends on what YOU are trying to depict.
Thukydides's post in Bosun, who scattered all this bloody mess on my bloody deck? was marked as the answer