Refer to "Clear Story Mode"

The only thing different here is you have to complete all the bonus stages, its nothing too challenging. In order to enter the bonus stage you have to go around the level and find 4 RED MUSIC NOTES. After you receive that last note you have to find the platform that will bring you to that bonus stage. You'll know you've found it because it will be glowing a blueish color and it will be shaped almost like a lillipad.
Most of the notes are easy but for the harder to reach one make your tongue useful by tapping
Note 1: To inform any confusion, the bonus stage is ALWAYS in the second part of the level. For example if you just beat level 1-1, it would be in *1-2*.
Note 2: There are always 3 notes on the first part of the level and 1 on the second part of the level.

Its just like "All that Glitters", search EVERYWHERE, sometimes they can really be hidden. You have to beat the game a couple of times so that you can find every balloon that you have to find. To make more balloons appear during the story do as stated--> After you beat the game once, save right after the credits and load up that saved game and then there will be more balloons to look for. The extra balloons will be describing the story a little bit more indepth.
Note: This has to be done in one play through, if you miss one balloon you have to start all over, so make sure you search, it will get boring but at the end it will pay off.

Below is a rerun of how many help balloons you should have at the end of each level (bonus stages included.)
1st playthrough
1-1: 3
1-2: 3
2-1: 0
2-2: 0
3-1: 0
3-2: 0
3-3: 2
4-1: 0
4-2: 0
5-1: 0
5-2: 0
5-3: 2





2nd playthrough
1-1: 3
1-2: 4
2-1: 2
2-2: 4
3-1: 2
3-2: 2
3-3: 0
4-1: 3
4-2: 3
5-1: 1
5-2: 4
5-3: 0