A bit of a struggle, this one, isn't it? The words are a bit ambiguous, and the precise meaning isn't entirely clear. I will say that they first put out the light, meaning the electric light. "Two candles were lit on the table" could have either meaning that you describe, but my feeling is that the writer intends to say (since it isn't a "dark sitting") that two candles had been lit prior to the sitting beginning, at the time that they were "directed to put out the light." When the lights were occasionally put out, my feeling is that the writer is saying that these candles went out and that this is one of the manifestations like the bell ringing and the accordion playing.
However, one could argue for other interpretations, as the writer doesn't state clearly which interpretations he intends.