"She eats an orange."
Translation:Ella come una naranja.
I do not know any rules but in general most words ending in "a" are feminine(or the plural "as". Someone posted that most words ending in L-O-N-E-R are masculine but I know there are "-ión" and "-ción" words that seem to be mostly feminine. Your going to just have to keep a few basic generalities like I mentioned in your head and memorize exceptions as you find them.
No, you are misunderstanding it. You can say in Spanish Ella come una naranja (literally She eats an orange) or Ella se come una naranja (literally She eats to herself an orange), both means the same. It would be different if you say Ella te come una naranja (literally She eats to you an orange) or Ella le come una naranja (literally She eats to him an orange).