I had this on CD and really enjoyed it. I've had the same question as yourself.
I always viewed the meditations you mention as cultivation exercises. While contemplating them, I've observed positive responses in my thoughts, feelings, nervous system etc. It's why I like them so much. So I just sit with it and allow that to be there. It reminds me of some restaurants and massage places that give you a hot, scented facecloth when you arrive for your face and hands. It's wonderfully refreshing.
So practically speaking (which is what you're asking), I think I'm just alternating in an unstructured way between the mantra, observing and enjoying the benefits I feel as well as periods of just breath meditation. Afterwards I tend to be loosely aware that I'm having a better day as a result of it. In a way it primes me to received the experiences of the day / night better.