i had a few 25m gaps in my survey area and used my plotter to define areas that needed going over, but next time I'm going to try taking a laptop out with RM on (I have wired in a 9 pin d-sub connector to the nmea 0183 output from my Lowrance unit - not difficult to do, just needs a very cheap 9-pin connector, a soldering iron and a usb to d-sub connector for your laptop). Will then run RM in live mode keeping an eye on the project contour map (which i think should update as you go), to try and get the area covered with no gaps.
Incidentally, Matt, a useful add on to RM might be an automatic survey planner - i.e. you put in a coastline / islands into the software, the maximum interpolation value you require, whether you want a 'box' or parallel line survey (and on which heading), start and end points, turning radius etc and RM works out track lines for you to follow on the RM projects display. WP's could also be exported within the work area to put on your GPS. Guess it would be quite a bit of work and I'm not sure everyone would want / need it, but id be very interested :-)