Essentially, the simple past tense and past perfect refer to different time frames when things happen. These time frames are relative to each other, not set times that stand on their own.
Which tense you choose would depend on the context and the time frame the main events are set in. There is no distinction when the sentences are taken out of context in the way you have done.
For example, if you tell a story or relate an event to someone using the simple past, then if you want to mention something that happened earlier, you can use the past perfect to express that.
Let's make up a little story for fun:
The phone rang, and my mother shouted "Billy, it's your friend Mary on the phone, and before you get into a long conversation, I want you
to clean your room this afternoon. I will not put up with the mess any
"Yes mum", I replied, although I had cleaned my room after I got up.
So, in the above story, the use of the past perfect tells us that the cleaning took place before the main events in the past tense time frame.
Note: I corrected the word "before" in your example, because it doesn't make sense to say you cleaned your room before you got up - because that would suggest you did it in your sleep!