上手い（うまい）means "dexterous" or "skillful," whereas 上手（じょうず）means "good"/"superior." They are both meant to compliment someone for being "skillful" or for having "superior" skills. I think what you are getting at is not that it is rude to use one or the other (うまいvs.　じょうず) when praising someone who is your superior (i.e., someone who ranks above you) in Japanese. It is a general cultural taboo in Japan to praise anyone who is your senior. The reasoning behind it is simple: If you are the person's junior, the idea is "who are you to judge someone superior to you?" By praising someone who is your senior, you are showing lack of humility, implying that you know better to tell someone who is your senior whether he is good or not. So rather than praising someone who is your senior in any way, you are supposed to say something like "大変勉強になりました”(I have learned so much from you.)