On the one hand, during the training phase (phone-level alignment, creation of acoustic models, henceforth AMs), the phonetic transcription provides information about where to expect recurring patterns in the acoustic signal, which will be abstracted away and generalized in the acoustic models for the individual (tri)phones.
during decoding, it mediates between (to borrow a neurolinguistic analogy) the top-down (predictive) processes based on the linguistic knowledge (the language models, henceforth LMs), and the bottom-up (recognitive) processes based on spotting acoustic patterns in the incoming sound data.