How to backup Mac Pro 2nd HD onto Time Machine

Hi, I have a Mac Pro with 2 internal HDs (1 x 500GB containing system and app files) and 1 x 1TB containing documents, pictures, etc.
I want to use Time Machine to store hourly versions of my work (especially changes to documents and pictures). How do I configure time machine to do this - at the moment it looks like it will backup everything from my home directory but not my second internal drive?
If I can't do this, what are the performance implications of having my documents (pages, keynote, numbers) being accessed from the boot drive - I understand that it is better to keep these separately.
Thanks for your help.

Actually, T.M. backs up any and you use to have to exclude a volume to not be included.
Also, I would still use another method for making a backup copy of your system and documents, like SuperDuper.
I don't see the need to backup the system except before making changes, patches, and updates or installing programs and such that I'm not 200% confident of, but otherwise I would not want to have the system and apps being backed up.
There are also utilities to modify T.M. behavior, when etc and to help navigate and inspect what is in T/M's backup archive.

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