How to upgrade my iPad mini OS? I have never upgraded iOS before and this is first time I would be doing. My current iOS version is 8.0.4(I guess) and want to upgrade to latest 8.x version(if possible) otherwise the default 9.x version as it's showing.

I want to know how can I take a restorable backup first on my Mac before going to upgrade? I am not so concerned about apps. My main concerns are books(Pdfs,epubs) that I open in iBooks app. Those app have not been bought within iBooks.

Is there anyway to take backup of books before I go for upgrade?
If you connect your iPad to your mac via its lightning cable and then open up iTunes, the iPad will show up as a device.

Click on it to bring up an info page that has an overview of everything stored on your iPad. From here you have to option to do a full back up by clicking the back up option. This will save all of your user data (including files added to iBooks app) in a back up to be stored on your mac. 

You then have the option to update iOS in iTunes, you can't update to 8.x unfortunately, you'll have to update to the latest version of iOS 9.x whatever that may be when you do the download.

Alternatively after you've done the backup you can unplug your iPad and download the update via wifi from within the settings app of the iPad.

Hope this helps