"I eat the meal with cheese."
Translation:Mi manĝas la manĝon kun fromaĝo.
"kun" is a preposition so it can come before a noun.
"kune" is an adverb, and so usually describes a verb.
If you want to say "with", use "kun": bread with cheese, pano kun fromaĝo
If you want to say "together", you probably want "kune": we danced together, ni dancis kune / ni kune dancis
If you want to say "together with", you can use "kune kun": I watched the film together with Marko, Mi spektis la filmon kune kun Marko.
Generally speaking, anywhere you would use "kune kun", you could also use simply "kun".