You reminded me of this fascinating group of people: http://www.vice.com/read/hanging-out-with-cannibals-georgia-rose-377
Ŝ is just 'sh' as in shock, shack, shore, etc. Ĵ is like the Z in seizure, L in leisure, J in soup du jour, S in measure, pleasure, treasure, Fraser and J in Jacques. Pronounced as zhər.
"Mi ŝatas fiŝaĵon en la supo." translates to "I like fish in the soup.".
This is because the soup you are talking about isn't necessarily fish soup, but some other type of soup with fish in it.
"I like fish soup." would most likely translate to "Mi ŝatas supo de fiŝo.".
"de" gives "supo" the property of "fiŝo", so "supo de fiŝo" literally translates to "soup of fish", which can be 'shortened' and made more easy to read as "fish soup".
Sure hope this clears things up for you!