You can have multiple data files in HB PC. For example, one for Lake#1 and another for Lake#2, etc. Then you can select/copy a waypoint(s) in one file and paste it into the other. When you have the points you want just copy that file to your SD card. To select more than one waypoint at a time hold down the Ctrl Key while selecting. For a range, select the first, hold the Shift key and select the last. The 'range' will be selected.
Remember, to keep from duplicating data in the HB unit, you should first 'clear all nav data' from the unit. I know this makes you nervous but if you're sure the data is safely on your SD card - and the PC - there should be no problem. Everything on the SD card will be read into the HB unit memory. So be sure you have a 'clean' data file with no duplicates before sending to the SD card and inserting into the HB unit.
Another idea: Since the unit will hold about 3,000 waypoints (I think) you could have all waypoints in one file and name them logically. For example I name points in FL's Lake Seminole as "SEMxxx" and Al's Eufaula as "EUxxx". Then when you look at the points by Name all the points similarly named will fall together. Suggest always use 3 digits after the 'name'. I separate my waypoints by region of the lake by using SEM1xx for one area then start at SEM2xx for another. Thus, not only do the Lake points sort together the regions on the lake do also.
Good Luck
