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The Church triumphant is the great company of holy spirits; the church militant is a congregation of men on earth, still fighting in the world against the devil and sin; the invisible church is the elect bride of Christ, known only to God; the visible church is mixed.
His disagreements with Rome were not only soteriological, but also ecclesiological. Yet his battle was not with the Roman Catholic Church, which he freely admitted was full of Christians; his battle was with the papacy, which he readily identified with the Antichrist.
So, how would one recognize the true church? The sincere preaching of the Word of God, and the lawful partaking of the sacraments of Christ. Yet, against these two requirements, if a church betrays an orthodox hermeneutic, it cannot be a true church.