We had a similar issue with building milestones. IMHO milestones in clubhouse are a way for a PM to interrogate the completeness of high level initiatives which are made up of epics. What was missing was the ability to organize a group of stories than span multiple epics into an iteration that the engineering team could push toward delivery. The iteration is a unit that the dev manager and team can use to track the completeness of their commitments. Recently clubhouse introduced iterations, to assist dev managers in tracking their deliverables.

I have never been happier with a tool and am excited to explore their new offering.