Blenky,
Let me give you an example - if you have a client machine with a single HDD on it and has four partitions C - D - E - F. Now if you want to encrypt only E and F. Then it is possible. No matter if you install SEE on C or on any other drive. To make this possible -- while you are creating client HDD package (on the server) then you need to specify which partitions you want to encrypt.
By default you have three options - encrypt all - encrypt specific partitions and let the user decide. Here you can choose second option and enter E and F. Install SEE on the client machine and by default SEE will encrypt only E and F. The access and recover utlity will also work fine. This example was for SEE 7.0.4.
Thanks