If you want to export waypoints at the same time as a map, you need to create a data set and add your map and waypoint set to this, and then export the data set.
If you are exporting directly from a map project, then unfortunately you can't export both the map and the waypoints to the same file straight from ReefMaster. What you need to do is export the map to a kmz file, then export the waypoints to another kmz (right-click on the set in the asset library). You can then open both these files in Google Earth and save the parent folder (usually called "Temporary Places"). This will give you a single kmz file with both waypoints and contours (you could create a new folder with whatever name you like, add your kmz files to that, and then save that in GE). You need a single kmz file for viewing on mobile.
With your contours - you do have minors, but they are hidden below a certain zoom level. They appear as you zoom in. You can change the level at which they appear by adjusting the "Show at zoom" slider in the GE export options. Move the slider further to the left to get the minor contours to show at a lower zoom level.
You might want to decrease your major contour setting and turn off the "fill shoreline" option also.
Matt