I can try and explain to you what I did. It's been a while though and I threw out my fender flares. I did go outside just now to take a look at my running boards up against the garage and think I remember some details.
The main thing I didn't catch initially may be holding you up right now. The running boards and fender flares have a rubber connector attempting to create that seamless look. You need to first remove these rubber accent pieces. Get up underneath the running boards and remove the screw(s) from the clip holding these rubber pieces to the boards and flares. They are sort of hidden, so look around with a flashlight if you need to.
Once these rubber accent pieces are off, you can detach the bolt/screw(s) connecting the flares to the running boards from above (no need to get underneath). The remaining screws attach the fender flare around its circumference to the wheel well and mounting bracket (these can be easily removed with a 1/4" socket driver, unless you remove your wheel and then it's obviously easier).
If this makes any sense, great! I hope I have helped out. Otherwise, if you plan on tossing all of the stuff you take off anyway, start tearing things off with brute force. ;-)