Get a few pieces of half inch pvc pipe and cut it to the width of the lumber on the edge and insert the tubing into the hole past the poly .Then add a bit of silicone around the pvc and the poly and it should be water proof and allow some of the excess moisture out .I have been in the window industry for years and we refered to it as a weep hole .Putting poly down is good , but condesation will build up under it from the moist soil and as you said in time it will be in need of replaceing .I don't want to tell you what to do , just something that I thought should be included with the roof design .We normally put a weep hole every two to three feet in a window , allowing condensation and any moisture a escape .Thats all I wanted to say 
