I believe they have the ability to transmit to each other at any given time, depending on the distance. Just like when they locked up that one Cylon and left him in the miniseires. They knew exactly where he was. As for Boomer, even though each one has the ability to have individual existance, they are still tied to each other's conciousness in some form. Notice that Boomer did not proclaim to be inlove with Helo until she and the Chief were broken up in Galactica. I don't even think that she felt that way until Helo suggested that he had feelings for her. With the Chief uninterested to continue their relationship, Boomer's mission to procreate switches it's attention over to Helo.
Also, we do know that each Cylon's memory can be selective. When Baltar did the test on Sharon, he was afraid that telling her would wake her up and she would in turn kill him for the knowledge that she was a spy.
The part I don't get is, is the Six in Baltar's head an implant or is it his own conscience making up scenarios? I was convinced it was the latter but when she showed up in the ship right as she disappeared from his mind confused the heck out of me. I mean, we know that she was physically there.