merhaba
in constant harmony i learned that if the word has more than one syllable, then the consonant at the end changes.

p becomes b
ç becomes c
t becomes d
k becomes ğ
And here are some examples to this:

kağıt-a --> kağıda (to the paper)

but in the present continous tense lesson i read this
when we want to say we are closing we say
kapat+iyor+iz and it becomes kapatıyoruz
so the question is why the last (t) in the word (kapat) didnt change to (d) ?
i hope you understand what i mean.
thanks anyway.

How do we know which verbs it applies to and which it doesn't??? Is there a rule or an indication in the dictionaries or something else?

I don't know if there is such a rule.
If you are not sure how to add any suffix to a word in accordance with the vowel or consonant harmony read it out, if it sounds nice it will be correct. If not there must be something wrong.

Didn't someone here once mention that it is indicated in some way in dictionaries when the consonant doesn't change? Just had a look in mine, but I can't see any indications. I might be wrong.. :-S

Anyway, there is always still the treasure that is called WinMekMak