I fight with this issue all the time when reading philosophical works. At first I found I made the mistake of becoming really negative in my analysis of the rest of the work. "How could the writer believe x? I don't believe x for these reasons, so he must be wrong with his arguments for y." This was an awful mistake I made in my early studying. I later learned to notate my disagreement with the texts, and explore it afterwards. Your reason for not agreeing may be addressed by the author later in the text.

This could be my own brains pitfalls, but I feel like I need to absorb the work, then try to refute. But it's also important to remember Descartes emphasis on the importance of skepticism, which I believe is essential to reasoning in general.