I recently transferred an OS "C:" partition from a HD to an SSD using this tutorial by whs
SSD - Install and Transfer the Operating System
I store my data on a different partition, and only have the OS and Programs on the "C:" partition.
I use Libraries to access my data folders and never had problems with this.
It sounds like you need to get your data moved to a different partition before migrating the OS and programs to an SSD.
You could also start from scratch with a clean OS (and programs) install to the SSD if you prefer.
How big is your HD, how big is the SSD you plan to get, and how much space is used for data on your "C:" HD partition?
Are you a gamer and have a lot of space used for games?
Most tech's store data on a different partition than the OS and Programs partition.
It makes backup/restore much easier...