My theory, and I hope the more experienced guys will check in with their opinion, is that you want the bait/lure moving through the water at about 2.5 to 3.5 knots (maybe a bit faster).
Going with the current, presuming a 3 knot current, to get that speed on the bait through the moving water, you need to have your boat going at 5-6 knots, as measured by gps (or a speedometer).
Against the 3 knot current, if the boat is held in one position, your bait, flashers, etc., are effectively already moving through the water at 3 knots, or rather the water is flowing over them at 3 knots. Put a couple of knots of speed (over land) on top of that and your gear is now effectively moving at 5 knots in the water.
That said, I usually just throw the gear in and chug about at various speeds, being the lousy fisherman that I am, but I think that the above explanation explains why one tack (or direction) of troll is usually more productive than others. Also I think that is why local practices for trolling patterns have evolved. We had a discussion here over the summer, where I recall Wolf commenting that - and I won't pretend that I recall it correctly, but the gist was that - at Renfrew the accepted pattern was for the outbound boats (heading northwest) had the inside shoreline route, whereas at Sooke, the inbound (southeast bound) boat had the inside shoreline right-of way.
Your best guide for correct speed, however, is always the action of the tackle in the water, and from that the angle of your downrigger wires, if you're using dr's.
Hope this holds water and helps. Sorry for the long windedness.