If you simply see किताब, it can mean both a book and the book.
वो किताब पढ़ रही है can mean -
She's reading the book.
She's reading a book.
As for using एक, you should use it whenever you would use it in English. There is no harm in using it and it only makes your sentence less ambiguous.
If my sister asks me -
क्या कर रहे हो? What are you doing?
I could reply with - मैं किताब पढ़ रहा हूँ or मैं एक किताब पढ़ रहा हूँ and both would convey the exact same meaning.
Since Hindi doesn't have the equivalent of 'the', you'll have to make do with 'that'. मैं वह किताब पढ़ रहा हूँ जो तुमने मुझे दी थी। I'm reading the book that you gave me. Here वह refers to the particular book that was gifted.