I am not sure I understand your question. Probably you are referring to the pause between the two speeches where the Imam sits down for a while. During this time most people ask Allah for forgiveness.

And Allah knows best

During juma, in the middle of the khutbah, the imam stops sometimes to say a pray for the prophet, and he does this out loud in Arabic. But then, sometimes, the imam will stop to pray in silence and everyone else follows this.So I’m wondering, what is this silent prayer? It seems like everyone else knows exactly what to pray and I’m always sitting there somewhat lost, . I’m new to Islam, so I’m just trying to learn everything I can.