It's true that in song lyrics or poetry you can more or less get away with anything, so why not?
However, 'to make something up' is a phrasal verb that means 'to invent a story'.
'To make it' means to succeed, so to express, 'reach the place that is over the clouds' you could simply say, 'Make it over the clouds'
If you do want to use 'up over' just bear in mind that it's not 'make it up' but rather 'make it' | 'up over'.
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