This is also a confusing problem for most of the native Korean speakers. They will understand what you mean even if you use in a wrong way. But actually, there is a slight difference.
계시다 and 있으시다 are both honorific forms of 있다. But they are used in different situations. 계시다 is the honorific form of 있다 when 있다 is used as a verb or an auxiliary verb. 있으시다 is used when 있다 is used as an adjective(In Korean, there is no be-verb. Thus, every word which means a state of a thing or a person is considered as an adjective).
거기 그대로 있어라/계세요. - In this case, 있다/계시다 is a verb.
이것을 가지고 있어라/계세요. - In this case, 있다/계시다 is an auxiliary verb of another verb, 가지다.
아버지께는 형님이 한 분 있다/있으시다. - In this case, the sentence can be translated into
There is a brother of my father's.
(This sentence is a little bit unnatural but I translated it in word-for-word.) 있으시다 in the sentence is a be-verb, not a normal verb. In Korean sentence, 있다 is considered to be an adjective. Therefore, 계신다 is wrong in this case.
Add) Steven's examples show a very important characteristic of Korean honorific. His example sentences show the difference between direct honorific(직접 높임) and indirect honorific(간접 높임). 계시다 is a
This sentence used 직접 높임 because the honorific form 계신다 is honoring the subject 선생님.
계시다 is the direct honorific form of 있다. 있으시다 is the indirect honorific form.