If you read Khenpo's 'Progressive Stages of Meditation on Emptiness' then this is complimentary to the Ngondro practices you are doing. It's all there.
Then read his songs of realization. The analytical meditations are important but so to is the understanding that the various views on emptiness are understood through practice more than just intellectual clinging. The thing I see more than anything is the idea that Madyamaka is just an intellectual exercise. This is far from the truth. You need to bring the analysis into practice to get an experience of what is being talked about when things are said to be appearance/emptiness inseparable and so forth.
The Blessed One said:
"What is the All? Simply the eye & forms, ear & sounds, nose & aromas, tongue & flavors, body & tactile sensations, intellect & ideas. This, monks, is called the All. Anyone who would say, 'Repudiating this All, I will describe another,' if questioned on what exactly might be the grounds for his statement, would be unable to explain, and furthermore, would be put to grief. Why? Because it lies beyond range." Sabba Sutta.