Congrats on the boat!!! What fun you will have! 

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We tried to anchor on the wreck a couple of times, but once the anchor fouled, and the second time we were dragging it, despite adequate scope.
It was decided to create a shot line and shot the wreck. The shot line had a fender at the top for a float. The three divers were dropped on the buoy and went down the line to the wreck.
On ascent, we came up the line, and surfaced at the buoy. Because of the wind, we had some surface current, and it was hard to keep station at the buoy. The boat wasn't far downwind, and my two buddies started to swim to it.
He was trying to position the boat so we could swim downwind to it, and it wouldn't be upwind and drift down onto us.
If you are ascending the line, is there any point in shooting a bag?
The captain of the boat was worried about a large tug and its towed ship, that appeared to be heading straight for our buoy, but I'm not sure an SMB could have been seen any further than the buoy, nor, by the time it was seen, could the tug have changed course. (The captain contacted them by radio, but by then, it was obvious they were going to miss us.)
Once the divers are on the surface, what is the best thing for them to do? Should they try to make for the boat, or stay with the buoy until the captain okays an attempt to reboard?
Who's in charge, once the divers are on the surface?
Or for things like areas with large tidal range or current possibly consider a top-tensioned shot to avoid needing loads of rope.
What's a top-tensioned shot? I would like to make a shot line to keep on the boat, and I've been puzzling about how best to do it.
I see pros and cons to anchoring. Certainly, if you're anchored, the divers have an upline and the boat doesn't have to run its engine while retrieving divers, which is much safer when the boat is small and the engine is an outboard.
The OP touches on another point about the dangers of diving in or near commercial shipping lanes. Please don't read this as an attack on the divers, but as a reminder that even if you do everything right there are other dangers out there.
Question- what would you have expected from the tug if it were on a collision course?
At the range that a commercial vessel can spot divers, surface marker bouys, or alpha flags flying on small boats, they are likely to be beyond the point where they can maneuver around them. This is especially true of tugs with tows, which already have severly restricted limited maneuverability.
It isn't a matter of right of way, it a practical matter of collision avoidence. I don't know about divers per se, but lots of pleasure boaters have died from collisions, despite possibly having the right of way, in crowded waters such as Long Island Sound, and other similar inland waterways.
You have to be extra cautious diving near shipping lanes, planning not only to avoid them, but also making sure that wind and current won't drift you into them, lest you put your captain in the difficult position of deciding whether to save his boat or save his divers.
I'm interested in the idea that it's preferable to have the boat upwind and drifting down on the divers. This is what our pilot was specifically trying to avoid. In current, it always seems that the boat tries to be downcurrent from the divers, and let them drift down on it; is it different in wind?