Follow these instructions EXACTLY and it should work:

• Open Dolphin Emulator (Make sure you're running 5.0)
• Right click on the Super Monkey Ball 2 game
• Select "Properties"
• Select the tab "AR Codes"
• Click "Add" at the bottom right
• Name it "Max Play Points"
• Put the code "0462A298 0001869F" (Do not include quotes and make sure there is a space between the 8 & 0)
• Click "Ok"
• Click the checkbox next to the "Max Play Points" AR code you just created.
• Click "Close" at the bottom right
• Click "Options" at the toolbar
• Click "Configure"
• Check the box that says "Enable Cheats"
• Click "Ok" at the bottom left
• Bootup Super Monkey Ball 2
• Go to "Party Games" and unlock every party game
• Go to "Options" and unlock every movie, the staff credit game and FINALLY the 99 monkeys (You will have to do the monkeys one by one which is a pain in the ass)
• Go to the main menu > Challenge Mode > Advanced
• On the Screen where your game is about to start move upwards to the "Monkeys" line
• Click X or A (whatever your action button is)
• You should be able to now change the amount of monkeys per set. Crank it up to 99 and your good to go :)

Let me know if you have any questions