There is a proper protocol in order to lodge a protest, just like there's a proper protocol to file a complaint with law enforcement or file suit in our legal system. You can't just stand there, point the finger and make accusations. And you can't wait beyond the statute of limitations. Doing so will only result in your protest going unheard.
First and foremost, judgment calls are not grounds for protest. This includes balls/strikes, out/safe, fair/foul, etc. Only the calls that involve the interpretation of specific rules are eligible to be protested. A manager lodging a protest must do so immediately. This means before play continues or the next pitch is thrown.
Per league rules
The $25.00 protest bond is in place to protect everyone in the league from frivolous protests. If you know the rules or are at least certain of the rule that was erroneously called against you and your team, lodge a formal protest so your case can be heard.In order to lodge a protest, the protesting manager must: 1) write a detailed explanation of the protest in the score book along with his/her signature, 2) have the umpire and opposing manager sign the score book, 3) be prepared to post a $25.00 protest bond. If you are not prepared to post this bond your protest will not be heard. If bond is posted and your protest is dismissed, your $25.00 bond will be forfeited. If your protest is upheld, your $25.00 bond will be returned and the game will be replayed at the earliest convenience to both teams from the point of the infraction.