"I wish you" should be followed by a noun, a thing -- not a clause or a sentence. So you are right, "I hope everything goes well" is better than "I wish you everything goes well." Examples that work with "I wish you..." include:
* I wish you the best of luck.
* I wish you great success.
If you want to combine "I wish you" with a clause (a "mini sentence," with a subject and a verb), it's best to use a "that" clause. Examples:
* I hope that everything goes well.
* I hope that you enjoy your new job.
* I wish that I could fly.
Note: with these "that" clauses, it is optional (in informal communication) to drop the "that" (although I always recommend that you include it, to avoid possible confusion). So it is usually not bad to say "I hope everything goes well," "I wish I could fly," etc.