A quick look through my CB&Q Waycar files yielded the following off of a Way Car Cupola detail drawing:
"Roof Covering: 1st layer of heavy roofing paper; top layer of #8 heavy duck layed lengthwise of car and lapped 1" on crown moulding and fastened with 12 oz. tacks."
This appears to be an as-built condition for CB&Q waycars which followed the same basic pattern from after the Civil War to the end of wood waycar use on the BN in the late 1970s. Very early cars might have had bare wood roofs but it is likely that canvas (duck) roofs were in use as I believe this was also common practice on passenger cars.