There are 3 upgrades per girl, making a total of 21 upgrades in the game. Upon getting an upgrade it is permanently activated and will display in yellow text on the girl selection menu.

The first upgrade next to easy can be acquired in either easy OR challenging, so you don't need to play both difficulties if you're going for 100% completion. This upgrade is obtained after surviving the first miniboss. That means that if a level is too hard for you on challenging, you can beat it on easy, play a bit of the next level, and then go back to the previous level on challenging.

The second upgrade is obtained upon completion of "challenge" difficulty. That's all for this one.

The last upgrade is obtained in the gallery. All you have to do is take a screenshot in a girl's gallery and you'll receive the corresponding upgrade. This means you can obtain it after completing the mission on either easy or challenging.

And that's all there is to it! Have fun!