Truecrypt System and Volume Encryption

Configuration:

Disk 0 - System [C] - [special library folders pointed to D]

Disk 1 - Data [D] - [changed to X for volume encryption process]

Disk 2 - Copy Data [E] - [mirror of D]

I have used truecrypt system encryption to encrypt Disk 0

I changed the drive letter of Disk 1 to X as I want to to mount this automatically with truecrypt on drive letter D when the system boots.

Should I have pointed the special folder libraries back at drive letter C before starting encryption of Disk 1, pointed them to drive letter X or will things be okay as they are?

Currently of course my libraries show as empty because they reference drive letter D not X. Not surprisingly I get an error to that effect when booting windows at the moment (i.e. "can't find D")

I am hoping that when Disk 1 [currently drive letter X] is encrypted and I set it to mount on drive letter D at boot then the current target for special library folders will have the correct drive letter to look at again (along with the data on Disk 1).

Only thing is that currently, if I attempt use drive letter D for anything [I was checking it out to see if it was free to use] I get a windows message saying the drive letter is in use. I can only think that this is the reference from C of the special library folders.

Does anyone have a view on this? I wonder if I am going to screw the referencing of the special library folders on C when I eventually mount the encrypted volume, Disk 1 [currently on drive letter X] on drive letter D.

Hope this all makes some sense to someone

NB
I am going to image C again before I attempt to mount disk 1 on D just in case.
As well as the mirror copy of data on E I have copies of my data external hard drives.

It worked.

Mounting the data drive on d following encryption has resulted in Windows recognising the location of special folders previously relocated to D.

The encryption and drive mounting processes have not got in the way.