The main problem for me was in terminology. There are Primary and Secondary Ingredients (plus Seasonings), and Basic and Supplementary flavors (labeled Primary and Secondary Flavors in the patch notes). A secondary ingredient goes in the secondary slot. The secondary ingredient could have a basic or supplementary flavor.
Basic flavors are: Sweet, Salty, Sour, Bitter and Savory
Supplementary flavors are: Pungent (spicy), and Astringent and Cool (minty)
Each level of recipe has limits on the number of basic and supplementary flavors. So far I haven't found a recipe that takes more than one secondary flavor (got to level 80 cooking on test). It would be nice to see these limits on the recipe window, but as you found out the results will tell you.
At lower levels you will want different flavors in each slot. Higher level recipes will allow you to repeat a flavor, but within limits, e.g. two sweet is fine with one or more other primary flavors, but three sweet will degrade because it is "Too Sweet."
It takes a variety of meat (or fish if you are piscivorous), vegetables, herbs and spices to make a good meal. Gather some and go experiment.