Having an architectural shingle roof installed in NYS. Grace Shingle-mate is the underlayment. For some reason they started with that at midroof and worked their way up, then installed the Grace ultra ice/water shield from eave up. Seems they were able to keep the overlaps always top over bottom as you look from peak to eave. Usually from what I know they go from bottom to top. I noticed there were a few areas where light shows through the Shingle-mate; probably due to the staples hitting a space between the old tongue and groove decking. Should i have them patch that over with some pieces of tape or water shield or is that normal? Where a porch hip roof meets a vinyl wall, can they install the proper flashing without temporarily removing the bottom part of the vinyl wall? Shall I assume that no black roofing cement should be used (tar?) on the chimney? Contract calls for step, apron flashing and back pan around chimney. Counter flashing against chimney to ensure watertight area, copperwork soldered etc. Where the upper copper edge is placed in between bricks pointing mortar should be used yes? thanks. I ask all this because some things have been done differently than I was told they would so then I feel I have to pay more attention.