If my fiancé stays overnight in a spare room in my home a few nights a week, would this be considered cohabitation?

Cohabitation generally refers to a man and a woman living together as husband and wife without benefit of marriage. In your case, allowing your fiancé to spend the night in a spare bedroom constitutes entertaining an overnight guest of the opposite sex of whom you have the expectation of marrying. It is not, in itself, sinful, but it can be a near occasion of sin and a possible cause of scandal.