Problem with matching coordinates from GIS to FEFLOW

Hello, I am a new user to FEFLOW and a rookie user in ArcGIS. I wanted to define the geological layers and aquifers. So, I had two files:
(1) Shapefile of the outline of the study area, and
(2) File with X,Y (northing, eastings), Elevation and Slice Number to define the points defining the stratigraphic layers.

Both of the files, I have defined their coordinate systems and they match up on GIS. However, when I move both into FEFLOW, they do not match up and I cannot set my stratigraphy. I found that somehow FEFLOW only took the elevation of one data point in (2) and applied it across the whole model.

Would appreciate any help! Thank you!

I assume that GIS projects one shapefile on the other shapefile, while FEFLOW simply plots the maps on its different native locations. Could you please try to plot each map separately in GIS and check the coordinates on the lower right hand side? I refer to the coordinates which are changing according to your mouse movement. I guess, the ranges of the coordinates are different. If this is the case, you need to transform the coordinate system. The coordinate system is usually stored in the *.prj-file. Please note that this file is not mandatory. If this file is not available and if you want to make a coordinate transformation you need to define the coordinate system to the input shapefile first.