Working around large boulders to create a habitat

Clearing a half acre lot to start a Pawpaw and Asian Persimmon orchard.  This will likely include other easy to grow fruit trees (no chemicals).  
I cleared the lot and discovered a lot of boulders. Some I can move around with my compact tractor and some I may have to bust up with expanding clay.
I have one large one in the ground and because of the clay it holds water in the moat I dug around it.  I have a pile of some others nearby.

Any ideas on how to make this a habitat for friendly snakes and lizards and other beneficials?  Should  I fill in the moat with dirt and pile the rocks on top or bury the rocks around the base of the big one?
Thoughts?

If it is holding water well, why not make it a water feature?   A mini pond can provide benefits to many creatures.   Plant around the edge to take advantage of the edge

Also, you could stack the boulders slightly apart but touching, with space underneath.  It would create shade and hiding spots

There is a natural well about 15 feet away.  It stays wet 11 months out of the year.
That will be a future project in making it look nice and attractive to the right insects and critters.
I could lean the smaller rocks against the partially buried rock but what about winter time? They would need a place to hibernate.

If this were mine, I would place the larger rock about a foot from the edge of the moat.  Then place smaller rocks against the larger rocks to make the habitat. Some small rock of different size in the moat so that critters can get out if they fall in.

Something like this: