If you sort your GSAK list before sending it to the GPSr, it will start at the top of the list and stop when it reaches the limit. For example, if you are caching near your house, you can set the center point of GSAk to your home and then export. You can also filter out caches you know you do not want to do like cache size, terrain, or distance using GSAk's filter until you have less than the maximum caches you want to send.

Alternatively, on most any of the export screens or macros there is an option which is "Maximum waypoints to send". Enter some number less than 2000 in that box and it will stop at that number (working it's way down the list.)