When it comes to groundwater flow modeling in complex geological settings one need to have different software tools. Recently I have discovered one very sophisticated path which I will share with you:
Build a complex 3D geology model in GeoModeller using geology maps, contacts, dips, drillhole data, cross sections… (see short description of this on link https://youtu.be/rLIOrhtwWBg )
Refine 3D geology model with geophysics again in GeoModeller, here is the video clip 6 min long about it – https://youtu.be/yjLvaoEIv5E
Translate 3D geology model from GeoModeller to FeFlow – here is how you can do it – https://youtu.be/cn-4zAXYU_Y
I think that this approach is giving excellent results integrating different kind of data in building conceptual site model.
If you are interested in live Skype presentation just send me an email and I would be happy to make demonstration for you.