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"Vicious Traditions" by The Veils.

A good number of crime scene detectives partake in exercise of some kind to clear their heads (and keep in shape). Atwood must've just chosen swimming as her form of exercise.

The presence of the Palo Alto investigators means she's going to Stanford. And there was a shot of Mr. Brooks driving into Menlo Park on his cover-up mission, which is right next to Stanford.

Mr. Brooks traveled to her college and did a copycat murder. To make it look like it was done by the same killer, he had cracked into the police database to look at the details of the crime that police would otherwise not make public. Since Jane had an alibi, she was dropped as a suspect, and investigators thereby assumed that there is a serial killer on campus.

A part of Mr. Brooks really did want to die. It wasn't all just an elaborate ploy to taunt Mr. Smith with hope, and then kill him. Mr. Brooks is battling an addiction that he knows isn't healthy, so naturally part of him wants to quit and part of him wants more. The battle within leaves him indecisive, so he set up a contingency plan in case he changed his mind, which he did. Probably this change happened when Mr. Smith mentioned in the car that he would expose Mr. Brooks to his family.

He wasn't. Mr. Brooks had his stuff moved to make Mr. Smith's disappearance seem planned, as well as to lure Detective Atwood to where Meeks and Sarah Leaves (Meeks' girlfriend) were hiding.

It was likely that Meeks would have killed Atwood, as Atwood was looking for Smith and was not expecting to find Meeks. This would have neatly resolved the issue of Mr. Brooks' #1 nemesis. Also, Mr. Brooks was very capable of 'sizing up' a person's psychological makeup as was revealed in how he read Smith like a book. Likewise, he also acknowledged Atwood's intense drive to be a success which included her obsessive pursuit of him, which he respected. This allowed him to foresee that Atwood would be pursuing Smith without backup after he had made her a suspect by murdering her husband.

It is also very likely that out of his respect for her. He gave Meeks up to her as "a gift". Much like Hannibal helping out Ms. Starling in Silence of the Lambs.

Mr. Brooks mentioned to Marshall that he respected Atwood for her choice to become a detective. He could have wanted to help her out out of respect (like he did when he killed her husband). But he also could've benefited from her death. Either scenario is possible; it's entirely plausible that he sent her to find Meeks with no real desire for either outcome and was torn between the choice, much like his decision at the graveyard.

He's honestly just intrigued about her. Brooks is very adept at 'sizing up' a person's psychological makeup and what makes them 'tick' as revealed by his reading Smith like a book. Yet it's this one aspect of Atwood that makes him wonder what drove her independence despite her father's wealth. Brooks' intrigue stems from his disappointment in his own daughter Jane for not having Atwood's qualities; puzzled by the ease she had with being supported by her father into adulthood instead of making it on her own. Lurking in Brooks' subconscious was a desire to more fully comprehend how he had failed in this aspect of fatherhood despite how it seemed obvious to the viewer that when it came to Jane he was in denial and blinded by his unconditional love to take care of her.

Another motive may have been ego, as most serial killers want to take credit for their work and enjoy taunting authorities as a means to 'prove' how much smarter they are by remaining elusive despite all their efforts, although he denies this is his motive to his alter-ego at the diner just before making "The Call".

Certain inheritable genes can make an individual more predisposed to psychopathy, but genes cannot alone account for a psychopath. Are there intergenerational families of murderous psychopaths? Such a theory certainly seems far-fetched, although there has not been enough study or data to prove or disprove this notion outright. Even had Jane inherited such a gene or genes from Mr. Brooks, given that she was raised in a seemingly safe and loving environment makes their expression in her personality remote unless triggered at some point by exposure to her father's 'addiction', she adopted the practice.

Not enough is known at this time about the science of 'addiction' to know precisely which environmental cues and to what degree of exposure is required before genes that predispose to 'addictive' behavior are triggered into individual expression. In other words, even had Jane inherited genes for psychopathy from her father it's not known what specific events need to occur and/or re-occur (e.g. would she need be a victim of repeated sadistic abuse or could merely her witnessing a live event of someone killing for pleasure like in the case of Mr. Smith act as a trigger? Can watching enough slasher flicks alone provide the inspiration for those predisposed?) for her to become a psychopath.

Marshall was Mr. Brooks alter-ego, who convinced him to keep killing. Marshall may have been a former victim, but it's not specifically specified.

In one of the deleted scenes, we learn that Brooks created Marshall in his head when he was younger.

In the original script, Detective Atwood (Demi Moore) tells Mr. Smith (Dane Cook) that she found clay on the carpet of the first couple's home. She doesn't mention that in the movie, however, but simply asks Mr. Smith if he makes vases or pots. The writers probably felt that Mr. Brooks (Kevin Costner) would not have made two obvious mistakes in a row, so it was left out.