I think that 'aversion' and 'desire' are opposite/complementary extremes of each other.
Similarly I think that 'delusion' is (defined as) the opposite of 'truth' (sacca/satya, the four noble truths) and (I presume) other 'true dharmas' (for example, one delusion might be a wrong view about 'self').
So I guess that you can be 'aware of delusion' whenever (if ever) you're aware that you have forgotten 'right view' or 'right mindfulness'.
If it's the 'root' klesha, I suppose it has many manfestations, but one of those is presumably any addictive behaviour: repeating the same harmful mistake.
You're right though that at the least the "The Four Frames of Reference" section of the Anapanasati Sutta only talks about "putting aside greed & distress with reference to the world". Maybe the parts of it after that i.e. "Awakening", "Knowing", and "Release" are describing the opposite of "ignorance".
Also, in The Taste of Freedom Bhikkhu Bodhi writes,
Three kinds of feelings have been pointed out by the Buddha: pleasant feeling, painful feeling, and neutral feeling, i.e., feeling which is neither pleasant nor painful. These three classes exhaust the totality of feeling, and one feeling of one class must be present on any given occasion of experience. Again, three mental factors have been singled out by the Buddha as the subjective counterparts of the three classes of feeling and described by him as anusaya, latent tendencies which have been lying dormant in the subconscious mental continua of sentient beings since beginningless time, always ready to crop up into a state of manifestation when an appropriate stimulus is encountered, and to subside again into the state of dormancy when the impact of the stimulus has worn off.
These three mental factors are lust (raga), repugnance (patigha), and ignorance (avijja), psychological equivalents of the unwholesome roots of greed (lobha), hatred (dosa), and delusion (moha). When a worldling, with a mind untrained in the higher course of mental discipline taught by the Buddha, experiences a pleasant feeling, then the latent tendency to lust springs up in response — a desire to possess and enjoy the object serving as stimulus for the pleasant feeling. When a worldling experiences a painful feeling, then the latent tendency to repugnance comes into play, an aversion toward the cause of the pain. And when a worldling experiences a neutral feeling, then the latent tendency to ignorance — present but recessive on occasions of lust and aversion — rises to prominence, shrouding the worldling's consciousness in a cloak of dull apathy.
Under the dominance of lust he is drawn to the pleasant, under the dominance of hate he is repelled by the painful, under the dominance of delusion he is confused by the neutral. He is bent up by happiness, bent down by sorrow, elated by gain, honor, and praise, dejected by loss, dishonor, and blame. Even though he perceives that a particular course of action can lead only to his harm, he is powerless to avoid it; even though he knows that an alternative course of action is clearly to his advantage, he is unable to pursue it. Swept on by the current of unabandoned defilements, he is driven from existence to existence through the ocean of samsara, with its waves of birth and death, its whirlpools of misery and despair.
So the three poisons (lust, anger, ignorance) correspond to three types of feeling (pleasant, painful, and neutral); and delusion therefore is associated with a "neutral" feeling, and "consciousness shrouded in a cloak of dull apathy" and "confusion".