you can consult the FLAC3D Manual " Example 1.12 Axially loaded pile — skin friction and end-bearing" for detailes on the modelling procedure.
you should know that once you create the soil grid and place the pile, the links will be created automatically. The default links are shown in section "1.10.1 Structural-Element Links". You can modify them or create your own with the command "sel link".
Did you try to use an interface element between the soil and a structural element? I am asking because I tried to join a shell element with a grid using the FLAC3D interface but the links were always created between the shell and the grid like if the interface was not there. In my opinion the FLAC3D's interface element is used only to join two grids, but there is structural elements which have their own interfaces like the liner element. This later behaves like a shell element with an interface.
And I did not understand what did you mean by "you should not consider the structural elements to be completely joined with the grids". Could you explain it please?