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.
I’m not sure about your elbow question, where are you planning to put that elbow?
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.