I'm pretty sure their village was on the island where the plane crashed, and that is how Goodwin was able to run there. They have an underwater hatch that could possibly link the two islands, and also a sub, it appears. They had a boat up until they gave it to Michael. From what we have seen on TV so far, the Others' village was on one island, and where Kate, Jack, and Sawyer are being held is on the other one.
Nah from the first clip of season 3 to me it looked like they were on a seperate island.
And as for this whole "only one boat thing" its fucking dharma or something close to dharma. Them having more then one shitty little boat is not completely out of the question. If I was stuck on an island I wouldn't give my only boat to people.