That majority of the folders that are in users/username you can right click on and change the directory where they are located. Appdata is not one of those folders but there is a way to link data to a folder on a separate drive but I don't know if appdata will work with that method or not but I don't see why it wouldn't... I forgot the technical term for that process.
Someone may have a better way for you to do this but if not this may help.
If you have a third drive I would start right clicking on those folders in users/username like mydocuments, music, pictures, desktop and start migrating them over to that other drive. Your goal I suppose is getting what is on that drive down to an amount you are okay with having on the SSD you may want to uninstall certain large programs that you don't need to be on an SSD. If you use steam you will probably want to uninstall it and then later re-install it with games that you don't need to have on the SSD on a separate drive and only the ones you want on the SSD actually there.
Anyways once the drive is trimmed down you could use one of the many available softwares to duplicate that info onto the SSD.
It needs to be capable of aligning it on the SSD (I think) and I think that paragon makes software that can move things from a standard drive to an SSD correctly. It will say so if I am thinking of the correct software.
Anyways I hope that helps and if no one else comes up with some better ideas or gives you the link to the process of linking the data on one drive to show as a folder on another drive then at least you know that it is possible to do so.
If you do a fresh install of windows onto the SSD then you can either use software designed for migrating data from another install of windows along with the method I said about right clicking on those folders and changing the locations. You may not have to do both.
From now on you know that desktop, mydocs, music, pictures, contacts, favorites, and more do not need to be on the primary partition at all which should make things easier to manage. After a new install you just right click on the new folders windows just created in users/username go to the tab that says location and select the location of the folder on the other drive.
Oh and I just copy the folder appdata over to the new install whenever I have to do something like that... which will not make your programs move over but will keep the majority of the settings once you re-install them.
Edited by givmedew - 6/8/13 at 9:07pm