We're getting ready to start it in the fall (one week). We're going to do once a week brain training along with daily exercises to help with the gate blocks. I have the reading program and I haven't read anywhere that you need to do two lessons a day - only one, which is broken down into different segments that total 45 minutes in length. We're not going to spend that amount of time doing the reading lessons (but my daughter is reading at or above grade level - I can just tell she's compensating for some mild dyslexic tendencies.) The one MAJOR area where the reading lesson goes against CM methods is that you're supposed to have them read word lists for 15 or 20 minutes - I can't remember which, but I think that is just TOO long to be reading only lists and THEN having them go on to read the story. I wouldn't have my child do that length of time, especially if it upset the child. If he/she enjoyed it, then I MIGHT do it for that long, but if they are enjoying it, it's probably because it's easy and they probably don't need to do it that long anyway.
Sorry, I'm not much help. I'm really looking forward to using this program, because I've heard such great things from people in our homeschool community as well as from my pediatrician.
I DO think you need to get the brain integration therapy manual in order to use the reading lessons most effectively. I can't imagine doing the reading lessons without also doing the exercises for the blocked learning gates. The good news, is that you should be able to sell the manual used when you're done - as it's hard to find used - so people are eager to buy it.