I didn't know there were the word 'comprehend' in English. So, I think I could translate my former sentence:
I can understand you, but I can't comprehend you (am I right?
)
On the other hand, on learning languages I think there are some stages. First you study basic structures (syntax) and some vocabulary. Later, when you are more or less competent with syntax and some vocabulary, you start learning another way of saying the things you say in your own language, you go beyond and learn new structures and vocabulary. Is in that point when one is able to think in the language he studies. Anyway, one must know the meaning of the words in his own language, because if you don't, you're lost .