Do a search on You Tube for: A Pillar trim Ford Flex.
I know you have an Ex but this video is the closest thing I could find.
One word of warning. The Flex supposedly has clips that allow the trim piece to slide out of (reference the video).
On my 2011 Ex, the trim pieces have different kind of clips, and you have to "Pop" them off. You said you had replacement parts already, so I'm assuming you have new trim pieces. So you can grab both sides of the shiny trim piece, wiggle and pull up at the same time and they should pop off. You'll likely break them, but if you have new trim pieces, no big deal.
If you don't have new clips to go with the new shiny trim pieces, be more careful in the removal. You should be able to save all the clips and not break them.
I had my windshield replaced today, and the shop told me it was likely they would break the trim pieces and I should get new ones. I figured if anyone was going to break them, it was going to be me. So I tried, and removed both of them successfully. Broke a plastic retainer on each side, but it's amazing what a little dab of silicone will do....
Most dealers are getting ~$100 a piece for them. Saw them as low as $85, but it is a Ford dealer only acquisition.
Good luck. Take your time, you'll be fine.