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I fitted a round piece of 1.5" foam into a cup holder, then cut a rectangular hole into the foam to hold my cell phone up. Think of a donut with a rectangular hole. It holds the phone securely, and it's invisible when the cover is closed over the cup holders.
I got one of those japanese cell phone holders that can clamp onto the A/C fins. I installed it on my center vent, the one on the passenger side. it works great. easy to pick up my phone, and still leaves lots of air going through the A/C outlet.