Use two Time Machine Drives with different settings?

Hello everybody, is it possible to use time machine with two drives and use different settings for each drive?
For example: at home I currently have two external LaCie d2 quadra drives. My plan is to leave one at home, and take one to Uni. On the drive which I have at home, I have backups of a secont parttion of the drive which I am taking to Uni, which contains some important files (about 500 GB). Is it possible to have a backup of that data partiton on the drive which I'm leaving at home, but not on the drive which I'm taking to uni?
I know that I can set up two drives to work simultaneously, but can I say to exclude folder A on drive A, but not on drive B?
Thanks a lot in advance

Thanks for the fast reply. II'll try to make things clearer. I have two drives (let's call them drive A and B). Drive A has one partition, and is my primary back up drive. Drive B has two partitions (one with files and one for Time Machine). Currently, the files partition of Drive B is being backed up to Drive A. When I connect drive B, Time machine asks me if I want to replace the existing drive, or use both. Using both is what I want. However, I don't need Drive B to back up the files from it's second partition, as that would not make any sense; I do, however, want drive A to back up the data partition from drive B. I guess the easiest way is to manually change the settings, or just live with a larger backup....

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