You actually have it easy. You'd clone your HDD to the SSD, then move your folders to the SSD. After they've been moved, make aliases of each folder, copy the aliases to the home folder on the HDD, delete the "real" folders and rename the aliases to match. In other words, when you make the aliases, they will be called "Documents alias" and you will need to rename it "Documents" when you copy it to the SSD location of your directory.
My problem was more annoying. I was given a 90GB SSD for work and I can't even load the OS and apps on it because I have too many. I think I actually think I have more data in /Applications and /Library/Application Support than the drive can handle, not to mention a whole OS with it.
You shouldn't have to "think" about what data you have where. You can very easily tell how much space any given file or folder is taking up by doing a "Get Info" on it. You can also use some software like "Disk Inventory X" to quickly get a list of all your folders and how big they are.
Unless you have some very specific needs I would think that 90GB is more than enough space for the OS and Applications. Personally I have Mountain Lion, XCode, Photoshop, and several other large software packages on my MacBook Air with a 64GB drive and it's only 2/3 full. The OS doesn't take THAT much space. A fresh install of Mountain Lion on an empty drive takes maybe 6GB, if I remember right.
For someone who wants to upgrade to an SSD, this is what I would do.
1) Buy a large external hard drive if you don't already have one. (You can get a 1TB 2.5" external drive for maybe $70 these days.) These are good for backups anyway. Now use a program like SuperDuper! to copy the contents of your current hard drive to the external drive. Now boot off the external drive.
2) Now you should have a computer with an SSD and hard drive that you can "re-pave" since all your data is on the external drive. I would re-format the internal drive into two partitions--one partition should be the size of the SSD and you can use it for backing up the contents of your SSD. The other should be for data.
3) After reformatting, copy all your songs/videos/pictures from the external drive to the data partition of your hard drive. Keep copying until the contents of the external drive is small enough to fit on the SSD. Remember, you can put infrequently used Applications on the hard drive too. You don't have to run applications from the SSD; it's just faster.
4) Now you should just be able to copy the contents of your external drive to the SSD (it fits now because you moved all your stuff), boot off the SSD, and you're done.