Number 2, "It is more fun to practice like that", is correct. Formally, "fun" cannot take the forms "funner" or "funnest" (although colloquially people may say "funnest"), unlike "quick/quicker/quickest".
If you say "It's funnier to practice like that" you are saying that it is more *funny* or more humorous, not more *fun. For example, "it is funnier to practice speaking with cartoon voices rather than our normal ones".
Edit: I just saw you're actually from the States too. So you get the whole thing about people saying "funnest" or "funner" colloquially.