There is no tool in GMS to do exactly what you want, but here's a possible workaround. There is an interpolation option to "Assign default extrapolation value to hidden objects". You can use that in combination with hidden mesh elements and the data calculator to create the type of data set you want. What you would do is hide the elements pertaining to the upper aquifer, then interpolate from scatter points to the mesh using the option mentioned above and a default extrapolation value of something like -999 or some number much less than you have in your data. Then you repeat the process but this time hide the lower aquifer elements and interpolate to the upper aquifer. Then you use the data calculator and create a new data set that is the max of the two data sets you just created which will get rid of the -999 values. You can then export that data set and use it for your initial condition.