Let me try to answer your question(s).
"The proposed channel contains the major storm with a minimum of 1 foot of freeboard. I have defined my bank stations where the grade breaks from 4:1 back to existing."
I understand this to mean that you have designed an open channel, probably trapezoidal, probably an earthen channel, with 4 horizontal to 1 vertical side slopes. This channel is sized to carry the "the major storm". I take this to mean that it is designed to carry the regulatory flood which is probably the so-called 100 year storm. That it also begins and ends at the existing stream and can contain the design ( 100 year) flow within the new channel with an additional 1 foot of freeboard.
You have now modeled this system of channels ( both new and existing ) using one of the five ways HEC-RAS allows encroachments to be modeled. Unsurprisingly, the flow is contained within the new channel but spills over the banks of the existing channel in several locations.
This means that the "floodway" extends to the edges of the flooded area, after the encriachment. Any farther encroachment would result in a rise in water surface of more than 1 foot. Remember that the "floodway" is NOT the same as the floodplain. The floodway may not be smaller than the bed and banks of the stream. In other words, you cannot fill into the stream itself.
This IS normal. You do NOT need to "tweak" the bank stations , and probably shouldn't try.
" but the county comments that we have received so far seem to indicate they want to see a floodway analysis through the proposed channel."
From this quote, it appears the County may not understand that the floodway and floodplain extents are the same if the flow is contained within the proposed channel.
Either that, or you have not modeled the entire system, includng both the existing and proposed channels. But, it appears you probably have done this.
You may be able to make this clear to the County by preparing flood plain maps of the area for the "before" condition and the "after" condition. You will eventually need a Letter of Map Revision (LOMR) which means you will have to submit your HEC-RAS data to FEMA, pay a fee, and wait probably 6 months to a year for a decision from everyone concerned.
good luck