For me (and I'm not as experienced as some), but the best way to read textbooks is to do a few passes first and get to know the material. I know asking questions right away is best, but like you I sometimes don't know where to begin. So I will do a pass or two and immediately the gaps in my knowledge will become apparent, which leads to questions. Once you've formulated the questions, it's amazing how Superreading will allow you to zero in on the answers in no time.
I think the difference between activating and skimming is 1) you have photoread before so your subconscious mind is already exposed to it (which you start to notice, the more and more you use the system and 2) multiple passes helps you absorb the material in a way skimming never did for me. You'll notice that if you do multiple passes (which at first seem like skimming), you'll eventually "gel" the material and be surprised at how easy it comes to you and how well you know it -- feelings I never got while skimming.
As someone who has struggled to apply the system to academia for some time, I think the best advice is when Paul says "keep pushing through" (highly paraphrased haha) -- basically if it doesn't make sense the first pass, go back and get another look at it.
