Two main points, I think, to understand here.
1. Samattha bhavana (kusala concentration meditation) can be very effectively done, even to the extent of the eight jhana by one who holds very strong convictions about self. This type of meditation may even lead to more fixed views about self (see brahmajala sutta). Now the actual view itself is akusala but the moments with true calm are kusala.
2. One can have right view, know with deep understanding that there is no self, and develop the same jhanas. One may still use the common parlance of me, I and so on. But one knows that these are simply designations, terms that are useful ways of communicating but that do not refer to actual realities. Thus one can still train "oneself", but understand that it is only by conditions that any kusala will arise - and thus one will not be perturbed if the kusala does not arise. Samattha and vipassana can go hand in hand - even for those who are sukka -vipassaka, dry insight workers (pure vipassana). For example, the development of vipassana makes metta -bhavana much easier. The far enemy of metta is anger but if panna is developed one can reflect easily "what am I angry with? Those namas and rupas that arose an instant ago have ceased already. Am I angry with the new ones? But these ones were not the ones that conditioned the sound that impinged on the ear sense. And that ear-sense and hearing consciousness have likewise long since passed...". this is just a very rough example of the type of reflection conditioned by the development of vipassana. This level of understanding allows metta to replace the anger. Lobha, desire, is the near enemy of metta. And for the true development of vipassana there must be good understanding of the characteristic of lobha - otherwise, as we often discuss, one will take refined lobha for sati. Thus as lobha is better and better understood, by developing satipatthana, one is less fooled by it also when developing metta.
Even though these aren't nama or rupa, is one more kusala than the other? Is there such a thing as a 'wise' or 'unwise' thought? And, if not, what was the Buddha's intention when instructing his listeners to think or to train themselves in such-and-such a way?
The thinking process is composed of namas and some of these also condition rupa. What is not real is the concept that may be the object of thought (purple elephants, mother, self, tables, cars, pretty woman....) The javanna moments are always rooted in either kusala (with amoha(wisdom) or without) or akusala. Thus we can surely talk about wise or unwise thoughts. When we consider Dhamma at the level of pondering the thoughts are to some extent rooted in amoha, wisdom, alobha, detachment and adosa, non aversion. (Ideally that is - we can of course be thinking about Dhamma with underlying delusion or attachment.) Right Understanding at the level of thinking is a crucial factor before deeper levels can arise. And too, as the direct understanding develops this supports more understanding at the thinking level. It is an unward spiral - wise thinking, direct understanding, wise thinking, direct understanding, wisethinking.... A very gradual upward spiral, cira kala bhavana (long, long time development). Even after vipassana nanas are reached (the real ones) wise thinking and study is needed to further assist wisdom to grow. The visuddhmagga XVIII24 says