Wadding of some sort was usually used, it could be paper, cotton, cloth, whatever was handy (I've heard of soldiers using grass). The wadding was usually put in after the ball, but there were exceptions.
Sometimes with cannons, wadding was placed in between the powder and ball, and then maybe some more wadding to hold the ball in place.
If the ball is tight fitting (on a rifle or musket), then wadding can be dispensed with.
A "patch" (typically of some sort of cloth), might be used, usually with a rifle. That would be pounded down with the ball, making a tight fit.
If using paper cartridges, the paper was left tied around the ball when loaded, serving both as a crude, and very poor, patch and wadding to hold the ball in place.
With the introduction of the minie-ball, patches or wadding to hold the bullet in place were found to be unnecessary by experiment (the tolerance was very tight, and the bullet would not work itself loose).
I think ships could be towed, and that was done if they were battered so much that they couldn't be sailed themselves.
Most sailing ships, even a pretty large one, can be manned by a surprisingly small "skeleton crew". You couldn't fight with such a crew, but you could sail the ship.
You need to a bit more specific about the "Colonial" period you are referring to -- as that could range from the early 1500s for the Spanish, to almost 1800. Things changed quite a bit, and there were also differences among the nations.
Traditionally, the "Master" was in charge of the ship, and the "Captain" commanded only the soldiers put aboard the ship. This was when warships were basically civilian ships that were commandeered for war. The title of the movie "Master and Commander" makes a reference to this ancient practice. Although by the time of that movie's setting the Captain was in complete control (thus the "and"). I think the Spanish carried on this practice in many of their sailing ships (i.e. Galleons) for longer, but I would have to double check.
This strange combination of different leaders could lead to complicated hierarchies. Also, there were many officers (and warrant officers -- another holdover) who were specialists.
Yes, sort of. Big ships could be relatively fast and maneuverable, or slow and cumbersome, depending upon whether they were built for war or trade (and big merchant ships like East Indiamen could be very well armed). A smaller ship will probably be more maneuverable; a bigger ship can put out more sail, and if the conditions are right might actually be faster. Some ships might be faster sailing into the wind than others, and vice versa. Ships also evolved, so a heavy war galleon might be reasonably maneuverable and fast for its day, might appear slow and cumbersome in Nelson's navy (and definitely under armed).
For an overview you might want to look at the old GURPS Swashbucklers book (which I think is good for circa 1700), or the GURPS Age of Napoleon if you are interested in the later period.