Question: I didn't understand why Darryl's rain business had been working (before the agents arrived). If Holt was the one who had been changing the weather, and he didn't like Darryl, why was he creating rain and allowing Darryl's business to be successful?
Answer: Because Darryl's success makes Sheila happy. Holt loves Sheila and is happy when she is happy. Ergo, Holt makes Darryl successful.
Answer: The rain were Holt's tears, not his happiness. Whenever Darryl did his rain dance, Shelia was in his corner, like a cheerleader, praising him. He caused a tornado, when she confessed her attraction to Agent Mulder.