modeling stone check strucutres

Under low-flow conditions, each check-dam will behave more like a small pond, with outflow over the dam, and perhaps even some seepage through the dam. This could be modeled as a series of ponds connected by short reaches.

Treating this as a single channel routing would only apply if you have normal Manning's flow throughout the channel. This would require sufficient flow depth so that the check-dams are well submerged, and can be treated as part of the overall "roughness" of the channel.

If these assumptions are valid, you could estimate the overall Manning's value using the table on page 128 of the HydroCAD Owner's Manual. You might use a weighted average somewhere between 0.04 (for irregular rock cuts) and the appropriate value for the rest of the channel. You may even be able to find a table that applies more directly to your situation.

If in doubt about the final value, I suggest a simple sensitivity analysis to see how accurate you need to be for the specific objectives of your study.