I can't cut up the magazines -- I always seem to forget something. I use the flags for specific patterns that I like. If I don't have anything marked in a magazine, they go to DD who passes those she does not want to a friend.
I have tried to keep the magazines organized, and I like your ideas. Unfortunately, when I look for a pattern I can't remember which magazine I found them in so I go through every one until I find it. Need to figure out a better system.
I do use binders for the EQ patterns or patterns/blocks I print off the internet. I have one binder for ideas and one for patterns that I have made.