I'm trying to determine which city my local taxes should be paid to. The LLC was registered using an address in City A however I rented an office and worked out of City B. My assumption is I should be pay my business income taxes to City B as well as employee withholdings.

Does that sound correct?

Most llcs are taxed as a pass through. So, I assume this question is based on an LLC that is not taxed as a corp.The llc needs to pay local taxes to City A , where the LLC was registered. where your business is physically located and what goods or services are you selling.