I think the issue is your projection.
Your soul map and the land use have different projection from your DEM causing the later not to over lay. Best way to fix it.
Easy way to get all the data you need is
2. Download DEM, LULC and Soil map bigger than your study area. Download the shape files of the exact area
3. Upload all to MAPSWAT after installation
4. Select clip shape files and choose your projection as Projected WGS 1984 and finish the process.
All map needed for your seat set up as well as the look up file will be available win your target folder.
Gafar Agunbiade
Ph.D. Student in Agricultural Systems Management,
Department Of Agricultural Sciences.
Clemson University.
Office/Lab: South Carolina Water Resources Center,
509 Westinghouse Road, Pendleton, SC, 29670.