One helpful strategy is to view your thoughts as if you were standing in a train station and watching the thoughts go by like cars of a very long train. The presence of the train or any particular car just is. It is neither good nor bad that it’s there.It could be, in a given context. Does your workbook provide one?
Following this analogy , can I say " the water is not yellow . It just seems.Sometimes "to be" is used with nothing following, to mean "exist(s)". That is correct. But that is not very common in English. "Exists" is more common. The phrasal verb "there is" is the most common.
Your example sentence adds "just" ("simply", "only"). Here "just is" is emphatic: the sentence says "not is good, not is bad, just is (exists)".