As soon as we could we got tarpaper down over the roof sheathing. (This is wet Western Washington after all.)
Then we finished up the wall sheathing, put the facia boards on the ends of the roof and covered it all with 90# roll roofing sealed at the seams (see next photo). This makes a great walking deck and it only cost about $38. At that price, if I have to take an afternoon to redo it in 5 to 10 years it won't be much of a problem. (Note, there are other roofing materials that can be used for these low pitch applications.)
This is a lower pitch than roll roofing is designed for, but it seals much better than asphalt shingles and we've had no leaks.