Please have a seat over there while you're waiting.
You can wait in that seat over there.
ーPlease have a seat over there while you're waiting.
「待っている間、あそこに座ってください」=「あちらに座ってお待ち下さい」
to have a seat で「座る・着席する」
ーYou can wait in that seat over there.
「あちらの椅子でお待ち下さい」
to wait in that seat で「あの席で待つ」
ご参考まで!