Both are valid words or expressions, but depending on how you use them, you may be making a mistake.
Cannot It's the formal way of "can't". Make sure to transcribe what the audio says, regardless of the proper way of talking (formal way or informal way).
Can not is part of a construction, where can precedes a second phrase that starts with not.
Examples with cannot
If the audios says:
[00:00:00] You cannot have dessert if you don't eat your vegetables
You should transcribe:
[00:00:00] You cannot have dessert if you don't eat your vegetables.
It would be a mistake to transcribe:
[00:00:00] You can't have dessert if you don't eat your vegetables.
[00:00:00] You can not have dessert if you don't eat your vegetables.
IMPORTANT: Can not, does not replace the word Cannot.
Examples with Can not:
Can not, with two words, is used as a connector.
- This new law can not only reduce the carbon emission but also can save millions of dollars a year.
- This console can not only run more graphics but also is lighter than other ones.
Usually, this "can not" is accompanied by "only" and "but also".