A friend of mine has developed a program to help people gain clarity in gemora learning:
I worked on a sefer like this.
R' Berkovits says the system assumes kids will kind of pick this up intuitively (he is kind of skeptical that this is the case). He says when your kids start learning Gemara, train them to pick up on the steps. This is a kasha, this is a teretz, how does the teretz answer the kasha? How does the raya prove the statement? A talmid of his started "Lamdeni" to help kids do this stuff.
Full copy of his shiur on this subject available by PM.