I have a brick and mortar businesses too and we pay local sales tax for each city or municipality where we are physically located. However, for my online store it appears to be charging state and city sales tax for the buyer. Is that correct? I'm worried that the city where I registered this business is going to come after me for sales tax. Also -- where is this collected tax revenue going? I'm using Shopify payments by Stripe.
I'm a state and local tax professional specializing in multi-state sales and use tax. Have you found the answer to your question? If not then if you'll give me more details about your transactions I can help figure out what is happening and whether or not it is correct.
I'm guessing the reason you pay local sales tax for each city where you are physically located is because that is where the customers are buying your products and taking delivery (or possession) of product as well. Or do you ship products to customers from those physical locations and still charge the local tax rate associated with your physical location. If that is the case please tell me the city/state of your physical locations. This will help me understand the sourcing rules applicable to your locations.
Is the online store charging tax for product shipped to different states (than the state of business locations )? If so are you reporting sales tax to those states?