Our EULAs typically allow you to install on 2 machines not typically in use at the same time. After that, we ask that you purchase additional licenses. Seperate partitions on the same machine count as one machine in my book. Just keep in mind that the more installs you activate, the closer you will be to tripping our activation system, and having to e-mail support to investigate and have your count reset.
To summerize, installing on both partitions will be fine.