Select the 1st waypoint. Scroll down to maybe #100, hold shift key and left click that waypoint. That will select all the waypoints in between. Right click on any highlighted waypoint and click Open. Next to "Display Mode" click the pull-down arrow and click the icon u want and all selected waypoints will now have that same icon. Next u could try maybe 200 waypoints etc until u get the dreaded "time out" then back off the selected amount.
The best way is to use MapSource. Seriously. BaseCamp really falls down here in that it's extremely slow and this is the only thing I use MapSource for now.