1) By default the list of enterprises to allocate to is set to only show open enterprises. To allocate expenses and revenue to crops from Initial Setup, you must use the Show Me button and select "Closed Only" or "< All >" for the filter labeled "Open or Closed". The list will then contain the Initial Setup enterprises you wish to allocate to.
Enterprises do not have to be open to allocate to them. Closing an enterprise only tells the program that farming should not record any more activity to this enterprise. When you re-open an enterprise, Farming will find the oldest open enterprise to allocate the inputs to.
Therefore, when you are done recording farming activity to the field go ahead and close the enterprise. Any expenses or revenue that are entered after closing can be allocated by selecting the enterprise from the list in Purchases, Sales, or Allocate Inputs.
2) Farm Fund$ does not have any way to track supply inventory at individual locations. It does keep track of total quantity on hand, and the method you suggested is probably the best way to record fuel inventory by location.
3) There should be no problem going back to initial setup to change or add to initial balances. The only time there will be a problem is when you go back and adjust the quantity of supplies inventory or harvested crops down to a point that would cause the total on hand to now be less than zero.
4) I am sorry to hear of any confusion the documentation may have caused. The online helps are continually being upgraded, and we are planning on having many more examples. Emphasis is also being placed on concepts and why the program does what it does.