Welcome to the forum!
It will help to know the brand and model of your two subwoofers.
It's not clear to me how you have everything hooked up. You say that both subs are connected to your Kenwood, but only one has speaker-level inputs and outputs. Does the second sub have speaker-level inputs but no outputs? Here's what I think you've done - connected the "A" speaker terminals from the Kenwood to one of the subs, connected the "B" speaker terminals from the Kenwood to the second sub, and connected the bookshelf speakers to the speaker outputs on one of the subs. Is that correct?