Once you find the wreck the first time, I think you can use a Nautilus Lifeline to get exact GPS coordinates. From what the rep told me at a scuba show once, you can send it up to the surface on a reel for a minute or two to get a position, and it will record the GPS position which you can download later to a computer with their desktop software. You only want to let out enough line on your reel for it to go straight to the surface and not drift down current
When you return and anchor, you probably want to put a float with just enough line onto the anchor so it floats directly above the anchor on the bottom. This should give you a relatively fixed reference point relative to where your boat ends up after you let out enough scope (probably between 3:1 and 5:1 depending on anchor type, how much chain you have, bottom type and current). You can then follow your anchor line down, or surface swim to the anchor float and descend, where you know the coordinates of the anchor on the bottom, descend and navigate directly to the wreck