Simple
Unsurprisingly the fingers don't have to be from the same hand or even the same person.
Choose two fingers that haven't been registered, middle and ring perhaps.
Open up touchID and select Add fingerprint.
ALTERNATE middle for one press, ring for the next, middle again, ring again.
Keep going and both prints will be registered.
Close off the phone, unlock it again with either of your new fingers!
UPDATE: My son has just managed to record four different fingerprints on on slot.
Simple
Unsurprisingly the fingers don't have to be from the same hand or even the same person.
Choose two fingers that haven't been registered, middle and ring perhaps.
Open up touchID and select Add fingerprint.
ALTERNATE middle for one press, ring for the next, middle again, ring again.
Keep going and both prints will be registered.
Close off the phone, unlock it again with either of your new fingers!
UPDATE: My son has just managed to record four different fingerprints on on slot.
This is not likely to work reliably. Touch ID is a learning system, and updates the reference scan every time you scan your finger. Having different non-matching references in one slot is going to confuse that. Either all but the one you use more frequently are going to stop working as it tunes the reference, or you may just get in a state where none of them work reliably. Touch ID already lets you record multiple fingers, and they certainly don't have to be from the same person. Why not use that functionality?
You're going to break it by doing this but, be my guest. Just don't come back posting "stupid touch ID doesn't work" in a few weeks. Some other user here had the same brilliant idea and he registered 2 fingers in the same slot and touch ID kept getting confused and validating neither set of prints in turn making touch ID not work properly.
I have been using multiple prints on one scan since the launch of the iPhone 5s. Have done so since I got my iPhone 6 in September as well. I have both thumbs registered as one and both index fingers registered as another. I have not had a single problem with my prints being read. You cannot break Touch ID. You can confuse it, but in my case no such confusion has occurred. That being said YMMV.
I have every family members toes setup for Touch ID. My family includes 2 dogs, 3 cats, 4 mice, 6 humans, and 14 hamsters.
Any reasoning for that given that separate slots can simply used for those?
I use all 5 slots. I use 4 slots for myself and I give one slot to my girlfriend (nothing to hide from her so I could care less, we've been together for over 6 years).
So it sounds like you are doing single finger for each of your slots based on what fingers you mentioned earlier.
How do u register your mice's paws on touch ID?