I would not do anything at this time. I think with winter coming on soon you need to just wait and then in February do the winter pruning. Next spring you can trim them periodically as you wish to shape the bushes to a desired form.
Knock out is generally virtually black spot proof. I am surprised to hear about your plants being affected by the disease as I have not seen such before on knock out. If the plants are very crowed and there is a lot of rain and/or sprinkler irrigation this can increase the incidence of disease on roses in general.
I am curious if your plants are a new color of knockout such as pink knockout or what. Our Q&A system is not set up to receive replies but you can submit another question to the Home Depot website with more info if you like and I will see it that way.
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