My suggestion would be to get stainless steel double wall pipe. Especially if the clearances to any combustibles is tight.
It is more expensive but I believe its worth it.
As far as the clean out tees go, I think they want one just above the fly ash collector to help trap any ash that may get past it. The ash will hit the tee and fall back into the collector.
I didn't do that. I have a very short run.
I went straight up with a 48" double wall telescoping piece off the collector up to the ceiling thimble where it connects to two 36" ss double wall pieces and then the cap.
The roof is low and I can jump up there and pop off the cap and first section to clean that. then I can pop off the telescoping piece and clean that out.
The last piece that is permanently attached to the thimble and roof flange is now easy to clean as well.
I didn't use any caulking because the double wall has a twist lock connection.
Sometimes a whisper of smoke may leak out of the connection between the telescoping pipe and the piece in the thimble.
But it really doesn't matter to me since I am outside in the garage.
And believe me the tiny amount that may leak out every now and then is nothing to the amount that will pour out of the firebox door every time you open it