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Vitakka, which Ven. Thannisaro translates to "applied thought", along with Vicara (sustained thought) is a component of first Jhana. Buddha spoke of them in singular item, vitakka-vicara. Let it go and we will enter second Jhanna.Jhanas
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Everything I've heard suggests that this is OK, though it's not ideal. Ideal meditation would be stillness without interruption of thoughts; handling words in the mind requires thought.
I recall an Audio Dharma podcast where it was suggested that if you must do this, try to keep the words as brief as possible "In breath." "Out breath." That sort of thing. :-)