I learned that for 존댓말 you should replace 있다 with 계시다, however it seems like most of the examples are in relation to where someone is (such as 할아버지께 댁에 계세요). Can you also use 계시다 for possession? Can you say 할아버지께 사과를 계세요?
No, you can not use 계시다 for possession. 있으시다 is used instead.
할아버지께 사과를 계세요
even if it would be used, it would be "가" or "는" instead of "를" (and usually 할아버지"는/가/께서").
할아버지는 사과가 있으세요.
Would be the most common form. Note that 사과 is technically the subject here, meaning that "계시다" would be showing respect to the apple. Funny, but probably not what you want!