I see two meanings for Yoku. Is the only way to decide which meaning to use by looking at the context they are used in or am I missing something? I also see Yokunai. Is this a 3rd word or just the negative of the Yoku meaning "well"?
The base is the "i" adjective 良い（よい/yoi）which means good. There are many ways to use it but basically the meaning will always be well or sometimes often(when in the yoku form). よくない(yokunai) is the negative and means not good.
よくない、negative of よい よく、meaning both well and often. To do something often, isn't that synonymous to doing it well?;)