Based on several articles (linking one below for reference, I hope this counts as a credible source), Manuel is the only one charged with the murder of Jonathan. There are 4 charged with the murder of Audrey, along with special circumstances of killing a witness. Manuel is also one of these 4.
There are 2 charged with accessory after the fact.
Man & woman charged in murder of missing couple plead not guilty
Someone posted information about this special circumstance charge - I don't know if it was on here or on reddit but I found the official link and posted herein - explaining that the charge is specifically for a witness to a crime different than the one they were killed during. The article explains that the witness cannot be killed during the same crime that he/she witnessed. Which rules out her being killed for witnessing Jonathan's murder, in my head.
Special Circumstances In Murder Cases
The second example given for this specific circumstance also stands out.
I have always believed that this was drug related but I don't think that Jonathan and/or Audrey were actually involved.
I know there has been a lot of talk about Jonathan potentially getting involved because he was out of a job and about to lose his apartment, but I don't think that was the case.
I unfortunately think that Audrey was the target, and Jonathan was in the wrong place at the wrong time. And I think that she was the target solely for having information about these people (this stems mainly from the special circumstance charge), especially knowing one was an ex and the woman was at one point a friend. I think that she may have turned a blind eye to some things that were going on during her time with Aaron, and he (and his friends) wanted to protect themselves once they knew she was moving on by dating someone else.
I am leaning towards this especially knowing there are more people being charged for her than there are for Jonathan.