If i install ubuntu as normal on the secondary HD, is it going to over write MBR/true crypt and screw up my main windows install?
Any help appreciated!
Yes, it will. I believe the only way to go about this is to fully decrypt the disk (using TrueCrypt in Windows), install Ubuntu dual-booting, and then set up full-disk encryption again. I believe TrueCrypt has native support for encrypting multiple operating systems now, but I am finding oddly little information about this online.