Most likely scenario prosecution:
Raf tells Amanda to carry a knife in her purse to defend herself, so she takes one of his kitchen knives. (please clarify for me if this knife was from her flat or his flat). For some reason, though he collects small knives and carries them on him at all times, he does not tell her to carry one of his extra ones with her. The night in question, he and Amanda were watching the movie Amelie. Amanda was supposed to be leaving momentarily for work, Raf had another appointment. At about 8:40 pm they both found themselves abruptly without commitments. They had just finished eating supper and were in a jovial mood, even though Raf's sink had overflowed yet again while cleaning up their dinner including fish, leaving stinky fish smelling water on the floor. (Or this is a false story that was backed up by the defendant's father to protect him). Now, abruptly without commitments they head over to the house to pack up for the trip the next day/fetch a mop/or to have a fun evening out alone. (perhaps they bring some food with them, and the knife to cut it with... makes more sense than carrying a kitchen knife in your purse). They run across Rudy on the way back. They arrive shortly after Meredith arrives, or as soon as she arrives. Rudy does drugs, perhaps he offers them something (lsd, ecstacy, something hardcore). They enter the flat and all chat a bit. Rudy has orange juice then goes and takes a dump. The scene becomes emotionally intense, either as the result of a confrontation (Meredith notices her rent money is missing, Rudy/all three become sexually aggressive to her, or she simply is annoyed and wants to go to bed). The result of this confrontation charges up the scene where she is restrained. Amanda and Raf join in restraining her. Then one of them begins to attack her with a knife and the other two spontaneously join in, stabbing her with their own knives. (Perhaps they were all playing a game with respective knives beforehand). They help to strip her, and Rudy continues the assault on Meredith's person as Amanda and Raf help him to do so, or withdraw to the other room. Abruptly, Rudy is afraid of being caught, and he flees the scene in his bloody shoes and clothing. (He may or may not have stolen from Meredith). Amanda and Raf realize how foolish they have just behaved. They have some blood on them. They do not want to leave any trace they were there. They go straight to the bathroom. Perhaps they were naked during the attack, which explains the lack of blood evidence on their clothing. But there is a shoe footprint (maybe) of Amanda and of Raf in the room, so they both had shoes on. They use the bidet and sink to clean off. Raf leaves a bloody bare footprint on the bathmat. Amanda takes a full shower. They then use the mop to carefully go over the crime scene, wiping away all the obvious evidence that they were there. They see the bloody footprint on the bathmat but hope it will be attributed to Rudy as getting rid of the bathmat would be too suspicious? Cleaning it off would be too suspicious? Amanda has a very trace amount of blood left on the bottom of her foot which leaves sporadic footprints that luminol will pick up later. (there is no evidence of smearing, or attempted clean up, so the clean up for what they could see was very good, but the footprints she couldn't see with her naked eye are not covered up). They cover up Meredith. They are worried that someone the next day will hear her phone ringing in the house so they go down the street and throw her phones into a garden (previous to midnight) and lock her door with the keys. They now need to establish an alibi, so they go back to Raffael's place about 5:30 am and turn on his itunes. They do a more thorough clean up here. They did not want the mop to be found at the previous scene, so they bring it back to his place. They thoroughly clean his place and the knife, though Amanda does not clean off the handle. They succesfully remove all traces of blood from the mop. (Or they cleaned up with the towel and just carry around a mop as part of an elaborate way of deflecting attention or something). The get rid of their own bloody clothes, and Raf's knife but choose to keep the kitchen knife in the drawer of the apartment. They think of leaving for the trip they were supposed to take, but worry that might make them look more guilty. They decide they need someone to come home to discover the crime scene. They go back and stage a break-in to justify calling someone without going into Meredith's room (or they did this between 12 and 5). They lock her room so it will make sense they were never in there. They hope Filomena will arrive and mar any additional evidence there might be. They plan to have her discover the body and enter Meredith's room with her to muddy the scene. They tell Filomena they called the police so she won't call them. The police arrive (surprising them) and start looking everything over. When they break down the door, instead of Knox and Sollecito being as close to the room as possible, (so as to provide a reason why there would be evidence of them in the room), they stay away from it, because the police are a surprise and they are nervous.
Once taken into custody, they crack under the pressure, deliberately creating false scenarios to look innocent. Amanda caves to the suggestion that Lumamba did it, since the police seem suspicious of him, and she knows that if Rudy is caught he will tell them she was there. Neither ask for a lawyer, because they are determined to look as innocent as possible. (they clearly don't watch CSI).
Alternatively: Amanda and Raffaele cleaned themselves up in the bathroom at the location, but did not clean up the location at all. They obviously had blood on them if they needed to clean up, so they still need to get rid of the clothing they were wearing. However, they assumed that all the evidence that was there of them would point to a burglar or Rudy.
But again, note: they did not now Rudy was a burglar, so they got lucky that their fake burglary happened to match up with the fact that he was a burglar. Not a stretch, because there aren't that many options at hand to justify calling Filomena and being worried.
I'll do my best case scenario for defense. I will note that it also has holes in it. I'd like to see a more likely proseuction case that explains the whole timeline better than I have (you can see the holes: why would she have a kitchen knife there? What circumstances would cause them all to spontaneously murder Meredith quickly? Why call Filomena before you have properly cleaned up the murder scene?) It falls further apart if we can 100% verify they called the police before the postal police arrived.
A note that Rudy's suggestion that it was about money can't be true since Amanda had over $4000 euros in her bank account at the time.