I am considering adding a electric windlass to my boat and I would like some
opinions on the best way to connect to the electrical system.

The windlass will be approximately 40 feet from my house battery bank

That means you need an 80-foot circuit sufficient to run a windlass. You're
talking some huge cables for a job like that.

Yes, consider putting in a separate battery for the windlass. If you can get
the battery within 5-6 feet of the windlass motor (without putting it in the
chain locker) you will be much happier.