You'll either have to set assigned starting locations which also requires you to pick at least the major civs that are going to be in the game directly in the map Edit Scenario (or Scenario) tab of Worldbuilder. I'm typing from memory so can't remember the exact designation of the various tabs within worldbuilder.
Otherwise you would have to make sure there are as many fertile areas on the map as there are ever going to be players, including CS players. Even then that won't I think be a guarantee there will be no 2+ players wanting to start in the same position issues.
Long-short is that WorldBuilder isn't as friendly as it could be for this sort of thing. It is much more a scenario-creation tool than it is a custom-map-with-random-start-posititions sort of tool.
And for determining fertile 'sweet spots', the game takes into account not only food-bearing tiles, but also strategic and luxury resources, as well as I think river tiles and grasslands and flood plains. Each of these different plots is assigned a 'fertility value' even though the tile in question may be a hill with a strategic resource. 'Fertility' in the sense the game uses for this calculation is really about how much value the tile has toward allowing a player to grow and become more advanced and more powerful, rather than directly a calculation of only food-yields.