Fantasy grounds has the column header 'Preparation', but how can you display whether a spell is prepared or not? Do you use the 'use column'?
If you simply update to the most recent version of the 5e module in Fantasy grounds, there are check boxes on the left side of each spell on the actions tab. You keep track of how many spell slots you have on the top.
TLDR; Top is spell slots, check boxes are prepared spells.
I think you tried to add the spells as powers, not as spells.
If you click the button on the lower right, there should be two options available 'add Spell' and 'add Power'.
Powers are something like Rage or Bardic Inspiration, which can only be used x number of times between two rests.
If you add the spells as spells you can change the button on the lower left to 'Preparation', then you can see checkboxes next to the spells. If you check them, and change the button back to 'Standard' or 'Combat' you should be able to see a little icon next to the spells prepared.
At least all of this should work in the latest version of the ruleset.