I think they were both very paranoid. I remember when Rudy was caught, Raffaele had admitted being afraid Rudy would frame him. (Why fear this if they had never met Rudy before?)
Another telling sign was Amanda said Patrick Lumbamba scared her but when asked she said she was not afraid of Rudy at all.
I do not think Amanda was afraid at all of being left alone. I really believe she thought he would turn on her, and she really wanted to know what he was asked and what he answered. I never got the feeling RS was afraid Amanda would turn on him, though she did once he took away her alibi. I think she always wanted to remain close to the investigation and monitor it's progression. There was no need for her to stay there at all if she was afraid of being alone, she would have gone home like everyone else did.
Another thing I find odd is that in one of her interviews (I think it was the very first one after she was released with Barbara Walters) when asked why she broke up with Raffaele she replied that one reason was he took away her alibi and the second was because they were in jail and not able to see eachother. Now in my opinion, if police really harassed her into falsely accusing Patrick, wouldn't she have the same logic as to why Raffaele took away her alibi? She obviously didn't and broke up with him. All my opinion