I think it is best not to mix Buddha Dhamma with concepts in Yoga or other Vedic teachings. As I have mentioned before, such teachings are distorted versions of the Buddha Dhamma.
– Even during Buddha Gotama’s time, such teachings were there coming from the Buddha Kassapa (the Buddha preceding Buddha Gotama). – A brief description of that at: “Arōgyā Paramā Lābhā..”
– As a reminder, there had been three Buddhas before Buddha Gotama on this Earth (i.e., during this Maha Kappa).
Question 1: Mano sankhara arise automatically based on our gati and the particular sense-object (without conscious thinking.)
– Then if we start consciously thinking or speaking about the subject matter, those involve vaci sankhara.
– If we go further and take bodily actions, those involve kaya sankhara.
– It is important to understand the types of sankhara; “Saṅkhāra – What It Really Means”
Question 2: What you are doing is exactly right. When negative/immoral thoughts come to the mind you need to shift the mind to the opposite of those (or at least to something different). That is the correct Anapanasati meditation.