Restoring partitions...but not certain changes

Here's my question:

1. I Make a full backup of my C (boot) drive (run Trueimage off a CD ur OSB drive to get this image. most data is on other physical drives).
2. Subsequently, use trueimage installed on the same C (boot) drive to make incremental or differential backsups.

Upon doing a full restore...excluding from the restored partitions changes I intentionally made after the first full image?

Note: To avoid being down for any length of time (over fifteen minutes) I have removable C drives that I periodically, (every four to eight weeks) make a full image, insert (recycle) another hard drive, and restore the previous image. Thus, I'm assured my backup image and restored work and, if necessary, I can take the hard drive from the previous cycle and re-insert. I would like to use incremental/differential backups, but I think this will force a restore of changes I intentionally made.

Thanks.