Hello,
For the topography file, you just need to add in your *.cas file:
BOTTOM TOPOGRAPHY FILE : name of your file here
This file accepts comments beginning by C and is read by subroutine FOND.f in library BIEF.
As for a file of water levels and flows, you can inspire from the example called 'culm', there is an example of LIQUID BOUNDARIES FILE, see the file t2d_culm.qsl. The only thing to know is the rank of every of your liquid boundaries, which is the order of appearance in the BOUNDARY CONDITIONS FILE.
With best regards,
Jean-Michel Hervouet