Time machine if partitioned disk

Hello,

I am currently using Time Machine in order to backup my iMac files. The OS X version is 10.8.5. I have my disk partitioned with two partitions. However I'm not sure if Time Machine will backup both partitions or only the main partition. Please your help because I want to remove the secondary partition and I don't know if I should copy the files or if Time Machine will backup those as well.

Thanks in advance

David V.