Yes, Sales Tax is a cart-based feature, and since Buy Now buttons bypass the cart to take a buyer directly to checkout, there's no chance to determine the buyer's location and apply tax calculation in the cart. Any function in E-junkie Seller Admin that says "Cart" in the link (Cart Sales Tax & VAT, Cart Shipping Settings, Cart Discount Settings) requires you to use our cart and View/Add to Cart buttons in order for those settings to work. :^)
You should not use tax/shipping settings at both ends (E-junkie and the payment processor) -- just one or the other -- but if you choose to try using tax settings at the payment processor's end, we have no control over how, or even if, those settings are applied during checkout, so that's entirely up to you to get working properly and troubleshoot any problems you may have. Also bear in mind that any settings in your payment processor account that pertain to a cart are referring to that processor's own cart service, not a third-party cart like ours.