If I transfer content from an iPad backup to a new iPad, are they synced, or can I change one without changing the other?

I have just bought a new iPad mini to use alongside my iPad Air.  They'll be used in much the same ways, just the mini being slightly more portable and the Air having a bigger capacity will have more content.
I'd like to set up my new mini from a backup of the Air (currently the Air doesn't have too much content that the mini will not have enough capacity), but then I'd like them to go their separate ways.  I'd like the mini to look how the Air currently does, but then I'd like to make tweaks to both of the devices, but in different ways to each other.  So, if I set up from back up and then delete an app or 2 off one, will it delete the apps off the other?
I assume they show up in iTunes as "iPad" and "iPad mini" or something different so I can use both devices with my Apple ID?
Or is it better to just set up from new and sync the bits I want to my new mini using iTunes.  That doesn't seem like it'd take so long, so might be easier?
Thanks!

You can restore the Air's backup onto the Mini - if not already in your computer's iTunes library then copy them over from the Air via File > Devices > Transfer Purchases (your iTunes downloads aren't included in a backup, the restore picks them up from your iTunes library).
Deleting an app off one iPad won't remove it from the other, and yes, when connected to your computer's iTunes they will show up as different devices (you can change the names that they show up as via Settings > General > About > Name) and what you subsequently sync to one of them won't be synced to other unless you choose to sync it.
If you will be using the same iCloud account on both then you can use Settings > iCloud to control whether your Safari bookmarks, contacts, calendars are kept in sync between the two.

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