Oh, well in that case:
- there already is a way to set your own checkpoints. Just press R to set a checkpoint wherever you stand. Pressing P resets it to the start too, just in case. I really wanted to make sure a single mistake never ruined your progress in the game. I get if that went unnoticed in the wall of text for the tutorial.
- And the upgrades are saved until the game ends. As long as the cloud of smoke is black, you still have the extra power. Not sure how to clarify that any other way. Maybe some more text. Hopefully there's no bug erasing your progress, because that definitely would be a problem. Another problem could be that it's not obvious you have extra power, again my bad.
In any case, thanks for clarifying what you meant!