I went to town today to get shingles. After I got back I put the felt paper on the top part. Kind of windy and not very warm (53 degrees), so that was a lot of fun. NOT!
Maybe I'm not seeing things correctly, but I'm thinking you need to "tuck" those bottom shingles under the polycarb. Or make a flashing and silicone under the flashing. You have to keep the runoff off of your wood.
Yes, the felt and the shingles will be over the poly on top and under the poly at the bottom. Like I said, I just laid them there to get a feel for how it was going to look.