Since the US is not classified as a risk area right now, you do not need to fill in any digital registration (see www.einreiseanmeldung.de). You will need to carry a negative test result with you, though, OR a proof of vaccination.

Since MUC is where you enter the Schengen area, you will have to go through passport control in MUC anyway (you would have had to do so even if you had been on a direct MUC-MLA flight). Customs will be in MLA.