For example say I have multiple substrate layers beneath a river at a bridge location. 10 feet of clay followed by 10 feet of shale. Is there a way to input multiple layers with different D50 values that would change the overall scouring during high flow events?
That is up to you as the modeler to determine. To answer your question, no, not within RAS or a HEC-18 spreadsheet can you do this. But if you receive a D50 at a depth of 10 ft and the calculated scour = 12 ft, then you must obtain a new D50 from a range greater than the depth calculated until it no longer supersedes your D50 sample depth.