OK so i figure every once in a while a RT comes across a ship that he decides he wants. For instance a lightly manned cruiser, that he decides to board and take. If this happens how would the players proceed to control this ship. Do all players need to be aboard and how would they lay claim to it inside the game? Is it even possible to control a fleet in the game? Those are my three major questions.

We've already overcome this issue, though it still needs to be worked out fully.

So far it has been a matter of blasting enemy vessels into submission. Basically cause specific damage types that cause fires, depressurizations and other hazards for the enemy crew, so that the enemy vessel suffers horrendous casualties and penalties to crew morale, and once the enemy vessel is dead in the water, we flood them with vox transmissions urging the enemy crew to rebel against their officers and commit mutiny and then contact us once the enemy officers are dead (otherwise we'll finish the job and vaporize their vessel completely).

Being a ship rating under such threats you'll probably choose whatever option you can that gives you a chance to live (especially when there are fires raging all across the boat and several hundres or thousands of your mates have already died under your current officer's poor leadership).

Once that issue has been overcome, and the enemy crew have hopefully done as we want, we go aboard the enemy vessel and start a bargain with the current "leaders" that might have formed among the workgangs and ratings, where we say that we're taking over the vessel and any and all crew members who wish to serve us. Anyone who wishes to leave is free to go once reparations are complete and we've managed to make port. Anyone who will accompany us will have to accept that we will change the personel rosters and that they might have to serve aboard another vessel instead of the current one (the reason for this is to make sure that all or most ratings find themselves in a new and unfamiliar setting with new and unfamiliar people so that mutinous groups with old allegiances don't form). However, if they accept and willingly serve they are granted better conditions and are guaranteed quality shore leave each time we make port (unless special conditions are in effect where we might not have time to stay).

Ratings aboard pirate vessels and such more often than not find these new conditions to be a vast improvement of the ones they had to toil under before, which means that given some time and the employment of some new ratings to cover the losses of the previous ones we have more or less found ourselves with yet another loyal vessel in our fleet. (though I should point out that this process has taken months if not years in in-game time)

Also, since we've been doing it a few times already, I should point out that im experimenting with an "upkeep system" that may or may not penalize the profit factor for the group for each new vessel they acquire. After all, managing ONE ship might be easy enough. Making sure that an entire fleet is running smoothly and efficiently however is going to cost you.

Kill everything on board, latch it to your ship with absurdly large chains, and drag it back to an anchorage for a refit and recruitment drive.

When my players found a near-hulked ship they spent some time refitting it with salvaged parts (They're not sure what wrecked the ship, but it took several others with it) and then transferred over some of their crew. The ships were similar sizes, so 1%= 1%. However as they travel to Footfall for repairs and re-crewing they're going to have a hard time keeping morale high, espcially on a near-crippled ship.