There is no need to change one's organization methods with LR. Just reference the files where they lay when importing and LR will mimic that structure in the Library as you know. This is the method I use. The only exception is that the files made from the raws will be kept in the same directory as the raw files.
The reason I don't just import from LR is that if I do so, LR will not match the file directory on the hard drive to what is shown in Library in the program. It'll place all shoots into the lightroom library directory on your hard drive instead. In addition, if you move an image from one shoot to another, those changes aren't reflected on the drive either (this happens regardless of how files are imported). Since the whole point in an open storage system is to make things easy to find outside of LR, I figure I'd minimize the mess as much as possible. It adds some extra work, but is worth it if I plan on using a different program with any of the files. This is something I hope they fix (I haven't tested B3 on this yet).