Analysing multiplex sequences, how to clean up and analyse individually

Hi, I’m working with a library that is composed of 16Sv3v4 and 4 bacterial housekeeping genes. I’m checking the FastQC but I don’t know if I have to trim them together or independently. Is there any workflow with some guide, that you could please share with me? Also, should I align them all together or will be better just to take the amplicon of each gene?. Many thanks.