How can you tell when the word "church" means the Body of Christ?

The word 'church' translates Ecclesia, which can mean any called-out assembly, not necessarily the Body of Christ. Paul almost always qualifies the present-day Church as the Body of Christ, saying 'the Church, which is his body.' Without that qualification, it may refer to Israel in the wilderness or an assembly.

Les explains that Ecclesia is used in different ways, so the word 'church' does not automatically mean the Body of Christ. Stephen called Israel around Sinai the Church in the Wilderness, though that was not the Body of Christ. In Acts, a riotous mob in Ephesus was also an Ecclesia, but translators called it an assembly. Paul, however, almost always qualifies the present-day Church as the Body of Christ, or says 'the Church, which is his body.' That qualification is the key indicator.

How does Paul make it clear that he is talking about the Church, the Body of Christ?

Paul makes it clear by almost always qualifying the present-day Church as the Body of Christ, adding phrases such as 'the Church, which is His body.' This distinguishes the Church, His body, from other called-out assemblies (ecclesias) also called churches, making clear he means the Body of Christ.