I have a 1000 sqft casita on my property and want to use it for my LLC, what is the best way to do this?

The 300 sq. ft. limit only applies if you are using the simplified method.  If you are using the regular method, then your home office deduction is based on the percentage of your office to your total home. If you are using your casita as a home office for your LLC, then this would be a separate structure and the expenses that apply to that structure would be the expenses that you can deduct if you use that space ONLY for business and use it regularly.

Whether or not you itemize does not affect what you can do with your home office neither does the account you use to pay for the mortgage.  There is not a benefit to using a business account to pay for the mortgage.  Even if you use your personal account, you can apply the applicable percentage to your interest and deduct it for your home office. 

 The Home Office Deduction