Best way to transfer old Macbook to new Macbook, both with two hard drives?

I am waiting for the new Macbook Pro's to come out, and I'm planning to upgrade my original 13in MBP. When I bought that MBP, I simply used Time Machine to copy my old Macbook to the new one. It work well.

But I've since replaced the hard drive with a solid state drive that houses the application and OS, plus some working files (photos), and I removed the optical drive and installed a large harddrive where I keep the user files.

I'm planning to order the new Macbook Pro with a larger SSD, and then replace the optical drive with a bigger hard drive, probably the one I currently have in my MBP.

What will be the best practice to transfer everything over. I want to keep most of what was on my old machine, inlcuding preferences, etc — but I also don't want years and years of junk transfered over. I've gone from Leopard to Snow Leopard to Mountain Lion, and so probably some junk from there as well, and I'm hoping that Mavericks will come with the new MBP.

Thanks for the help!