Problems finding the next empty cell and paste value

Try this:

Sub CopyData()
    Dim lr As Integer
    With Sheets("output")
        lr = .Range("B" & .Rows.Count).End(xlUp).Row + 1
        .Range("B" & lr) = Sheets("input").Range("B5")
        .Range("C" & lr) = Sheets("input").Range("C5")
        .Range("B" & lr + 1) = Sheets("input").Range("E5")
        .Range("C" & lr + 1) = Sheets("input").Range("F5")
    End With
End Sub

Why don't you just format the entire column instead of doing it in the macro?

Otherwise you can do it like this...

Sub CopyData()
    Dim lr As Integer
    With Sheets("output")
        lr = .Range("B" & .Rows.Count).End(xlUp).Row + 1
        .Range("B" & lr) = Sheets("input").Range("B5")
        .Range("C" & lr) = Sheets("input").Range("C5")
        .Range("C" & lr).NumberFormat = "[$€-2] #,##0.00"
        .Range("B" & lr + 1) = Sheets("input").Range("E5")
        .Range("C" & lr + 1) = Sheets("input").Range("F5")
        .Range("C" & lr + 1).NumberFormat = "[$€-2] #,##0.00"
    End With
End Sub