1) これは ねこですか。(KORE WA NEKO DESUKA) = Is this a cat? 2) ねこは これですか。(NEKO WA KORE DESUKA) = Is a/the cat this one?
These two sentences are grammatically correct, and they have basically the same meaning. However, they can be used differently depending on the situation.
(Example 1) There is a little girl drawing something. You don’t know what she is drawing, but it looks like a cat. You point to her drawing and ask her;
これは ねこですか。(KORE WA NEKO DESUKA) = Is this a cat?
In this situation, the first sentence sounds more natural than the second sentence. What you are talking about is これ (KORE/this), which is the topic of the sentence. What comes after は (WA) is a description or a question (ねこですか/NEKO DESUKA).
(Example 2) The girl says, “I am drawing a dog and a cat.” When she is done drawing, you point to one of the objects she has drawn and ask her;
ねこは これですか。(NEKO WA KORE DESUKA) = Is the cat this one?/As for the cat, is it this one?
You know that she drew a cat (and a dog). Therefore, ねこ (NEKO) is used as the topic of the sentence. Of course, they understand even if you use the first sentence instead, but it is just that the second sentence sounds more natural in this situation.
3) どれが いぬですか。(DORE GA INU DESUKA) 4) いぬは どれですか。(INU WA DORE DESUKA) = Which one is a dog?
As for your third sentence, the particle should be が since it starts with the question word どれ.
Both #3 and #4 have the same meaning. They can be used differently depending on the situation just like #1 and #2.
When learning Japanese using book 1, it would be better to focus on how to make sentences correctly, rather than when and under what circumstances you should use one or the other.