It is my understanding (I’ve dealt with in-house engines and it works this way) that you pay Epic 5% of ANYTHING your game makes and Epic is the top of the stack, for example lets say your game makes $100, you give Epic 5% (which is $5 in this case), then you give Steam $30, which is 30% of the original value the game made. As far as I’m aware percentages given to any middlewere/companies you use percentages are based on the original values made and not after operating costs. Now Epic lets you make your first $3000 per year without owing 5%, so once you’ve worked out how much you have to pay them, you take $3000 off.
If you have further questions I’d recommend asking Epic directly, just know that Epic asking for only 5% for allowing you to use their engine is absolutely amazing and only 10 years ago you’d be looking at 30% - 50% of your profits for a AAA game like Unreal Engine.
edit:
I need to add that you should also double check what plugins and middlewere your game uses and make sure you don’t need to pay them anything or come to any license agreements (a usual clause is that you include their logos in splash screens), check license agreements on each respective system, for example if you use SpeedTree do check that you don’t need to pay them a percentage of what you make. SpeedTree may have changed their licensing agreement since I’ve worked with it but it used to be the case that you had to include their logo in a splash screen and any credits and It’ll be safe to assume that this is still the case.