There may be non-free books or documentation files that describe the program you are documenting.
It is ok to use these documents for reference, just as the author of a new algebra textbook can read other books on algebra. A large portion of any non-fiction book consists of facts, in this case facts about how a certain program works, and these facts are necessarily the same for everyone who writes about the subject. But be careful not to copy your outline structure, wording, tables or examples from preexisting non-free documentation. Copying from free documentation may be ok; please check with the FSF about the individual case.