I am sure that there is a good practice for saving the raw data from the sonar. I haven't been good at being systematic at saving all my files that I have used to build my maps. I am new and learn from all of you. I have a very good map now to fish with and want to be able to rebuild it if my hard drive crashes. That being said, what is a good practice when I come in and I have a gig of data on my SD card from fishing and want to first save it permanently,then secondly add the tracks to an already good map that has a few small gaps in it?

I have around 1700 GB of sonarlogs and tracklogs stored. I use an external harddrive for this, with another external harddrive as backup.

I sort my data after lake-equipment. So right now I have about 70 folders named after the lake the data was recorded in. In each folder I have folders named "TM150M, "P66", "HST-WSBL" etc, containing the actual sonarlogs.

I also have a spreadsheet (Excel) where I keep track of waterlevels in the different lakes where such data is available online. Every sonarlog is adjusted according to the waterlevel.

Do you review the sonar logs to mark structure to explore? If so, do you have a means to relate a waypoint created from the sonar log back to the originating log file (and location inside that file)? I'm thinking about waypoint management methodolgy and systems.

The way I do it is as follows, I have approx 1300 sidescan logs, many of which have marine archaeology appearing.

I save each track as a date and place, for example the 3rd run of the day in kilbeg would be called 3March2015Kilbeg3. Waypoints are not exclusive to a particular logfile, the structure will appear on many sidescan swaths, so I use a graphical database to display the entire set of tracks (not swaths) in an area, and can then pick out tracks which will intersect the relevant waypoint. Waypoints are generally the result of an aggregation of points. Similarly, if I'm looking for an area to survey I can base the survey on previous tracks, and cover an area at a new angle over new ground.
I use RM to analyze the swath and to grab georeferenced images of the section I'm interested in, these then go into the dataset for each waypoint. Each waypoint has its own folder which will contain all of the information relevant to it. I can use these images on survey charts to position myself exactly over whatever I'm looking at / filming or to run along it on the course I decide will give me optimum angles for sequences.
The interconnection of data can be quite tricky, particularly once you build up datasets with a wide variety of formats (sl2,sl3, gpx, jpg, mp4, drd, doc) etc all relating to one specific object.

Yes I use both SS and 2D in Reefmaster to make waypoints. But I use Insight Planner for WP-organization, so I just move them there when I'm done in RM. (IP has the correct WP-symbols.)