kobo glo direct filesystem content modification

Hello

I just got an kobo glo hd, I would take the sd card out of the device, mount it on my computer and modify the scripts, add binaries, etc.
I've seen that there is a file called /fs.md5sum, I guess i need to update it after modifying the filesystem contents.

I would modify a KoboRoot.tgz to make it do what I want, but I cannot found one the same version as my current ROM, 3.16.17 bcc6ad7496 7/30/15.

So, my question is, can I modify the root filesystem contents? what's the second partition used for?

thanks