You may use this in both situations, and indeed in others; the context will make it clear which meaning is intended:
If you ask before you start preparing the coffee, you are asking how your hearer prefer their coffee to be prepared—Do you like it strong or weak (or possibly boiled to a black sludge)?
If you ask before or as you serve the coffee, you are asking how your hearer 'takes' their coffee—Do you want cream or sugar with your coffee?
If you ask after your hearer has started drinking the coffee, you are asking about the taste of the coffee—Is the coffee OK?