I apologize but I don’t understand your question… or rather a description of your setup installation.
Correct me if I’m wrong:
You have a water heater and a hot water heating appliance (a boiler) connected to a chimney. The chimney has a 6” diameter flue liner.
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I’m not sure about your elbow question, where are you planning to put that elbow?
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Is it going to be on the connectors (vent pipes) between the appliances and the chimney liner?
A cleanout is usually installed at the base of a chimney or some distance below where the connectors from appliances penetrate its wall, not between them.
Please explain your installation with some more details, just click “comment” below.