If Charles is really the mystery A, I have a theory that might work. Feel free to poke holes if you can,I don't mind! If it doesn't work, it doesn't work. :)
Mr. Dilaurentis and Marion Cavanaugh had an affair which resulted in "Charles." They panicked and decided it was best to put him up for adoption, some place far away (Maybe another country?) no one could know about the affair. Marion suffered extreme guilt which eventually broke her down and resulted in her stay at Radley. At some point Mrs. D joins the board. She has known Marion for years, and being the nosy person she is, she looks into Marion's Medical files to snoop. She then learns about the affair and the child. She's livid. It gets to the point where she can no longer pretend she doesn't know. Thinking she would be alone, She lures Marion to the roof to confront her. She doesn't see the "fragile patient" -Bethany. Mrs. D and Marion begin to argue, it turns physical, and mrs. D shoves Marion. She falls and dies. Bethany screams, and Mrs. D then realizes she saw everything. She couldn't kill her, so she did the next best thing, and played on her mental illness, convincing her she didn't see anything (just like she did with Ali and the dresses.)she begins to buy her things, and take her on outings. Bethany loved it at first, but soon she started having memories about that night. She finally confronts Mrs. D about what she remembers. Mrs. D becomes angry and tells her she's crazy. This is when Bethany starts the angry drawings, calling mrs. D a liar, etc. Meanwhile, Ali is wondering why Mrs. D has become so attached to this, "crazy Radley patient." As we know she is extremly jealous. She starts doing her own research and even has Cece check herself into Radley so she could get close to Bethany. Eventually she figures it out. She invites Bethany to Rosewood, mother like daughter, she plays on Bethany's need to feel wanted. But before Bethany's arrival she needs to get rid of Toby, what if Marion had told him about the affair. She throws the firework but injures Jenna instead, she blackmails him to take the blame, and he is sent away. With Toby out of the way she continues her plan to lure bethany there. On the night of the murder she confronts Bethany. She may or may not attack her, But she feels like she scared her enough to keep quiet. she then heads home. But Bethany isn't afraid and follows Ali to her front yard. This is when mrs. D witnesses Ali get hit with the rock. Mrs. d, or the liars(remember they are drunk and drugged), see this and kill Bethany on accident. They didn't know about the previous confrontation. Now Ali has to get out of town. Her mom knew she was alive the entire time, that's why she was still buying her clothes, etc. Now for Charles. He could be a few characters, but for this theory I'm going with Wren. He discoverd he is adopted, and hires a private investigator (possibly James Neilan) to track down his birth parents. He finds out his mother is dead, but his father is alive in Rosewood. He moves and tries to get close to people who know his family. He finds out he has a brother, Toby, and that he is close to the Hastings. He targets Melissa first but doesn't get much from her, so he goes after Spencer next. After Mona's game is revealed he takes the job at Radley, he's curios about Mona's motives, and also wants to learn more about his mother. He discovers that there is something suspicios about his mothers death, and that the liars have a lot of secrets. He now has access to Mona's secrets, and also medical records. He sees Bethany's drawing of Marion "falling" from the roof and starts to put it all together. He's furious and wants revenge, he then decides to take over the game Mona has created. The first thing he does as "A" is send Toby clues about Marion's death. He wants Toby to know it was not sucide, he wants to help his brother. (This is the first time A ever offered help) As we all know there is so many clues that tie Wren to A. I couldn't think of a motive until now. Think about all that's happen. Wildens death could even be because he doctored the documents about Marion's death. (There is also a sign in sheet that had the name C.Cavanuagh. Charles would technically be both Dilaurentis and a Cavanuagh.)