Here's what I was able to figure out on my own:
1. Open Map Finder from the desktop. From the file menu, choose Rule Builder.
2. In the Rule Builder, you will see several pre-made groups, with rules in each group. Later, when you run Map Finder in Civ4, Map Finder will save any start that meets all of the rules specified in a group. You can Add/Delete groups and rules with the buttons on the right. If you click on a rule, you can change that rule using the drop down menus at the bottom. You can make a rule to look for a certain number of flood plains, or freshwater corn, or pasture resources, etc... Be sure to specify the Min and Max of that type of tile/resource you're looking for. After you've built all of the groups you want Map Finder to look for, save your changes.
3. Close Map Finder and start up Civ4. Start up a game with your desired settings. After the game begins, press Alt-M to start Map Finder. You should see the game begin to Regenerate the map, over and over again. It will keep a running count of how many games it has regenerated, and how many of those it has saved (because it fit one of your groups). You can change the maximum number of regenerations and the speed of regeneration in the Options menu, HOF3 tab. Let it run for a while (unfortunately, it wont run in the background). When you want to take a look at the saved starts, press Alt-X and quit Civ4.
4. Open Map Finder from the desktop again. Click on the Civ Version Menu and choose the Civ version you are using. The saved games should display in the rows below the resource icons. You'll be able to see a screenshot, and the table will list the resources that appear in the shot. If you're ready to play one of the saves, you can rename the weird file name and move it to a desired folder.