You need to add the snap pour point very intelligently. Sometimes the hit and trial method is the only way around. In theory, the snap pour point is the output location where the whole of the upstream area pours water into. Think on these lines, I hope you will be able to solve this issue.
May be the ArcGIS version it matter. so, try it by changing the ArcGIS and HEC-geoHMS version such as Arc-GIS 10.6 with Hec-GeoHMS10.6,and heArc-Hydro tools 10.6. You can download here http://downloads.esri.com/archydro/
We've recently added GIS tools directly to HEC-HMS. We did this in an attempt to make the model creation process easier and more efficient. As such, there's no need to use HEC-GeoHMS and/or ArcHydro anymore to create input files. For further information, check out these videos: https://www.youtube.com/playlist?list=PLH7yUh2l8q9WKAraul4EatMMPh0ayNtQY. Also, check out these example applications: https://www.hec.usace.army.mil/confluence/display/HMSGUIDES/GIS+Tutorials+and+Guides. Let me know if you have any questions.