Yes, you will need to make a small change in the dyn_em/module_initialize_real.F file. Look for this loop:
DO j = jts, MIN(jde-1, jte)
DO i = its, MIN(ide-1, ite)
IF ((grid%landmask(i,j) .LT. 0.5) .AND. (flag_sst .EQ. 1) .AND. &
(grid%sst(i,j) .GT. 170.) .AND. (grid%sst(i,j) .LT. 400.)) THEN
grid%tsk(i,j) = grid%sst(i,j)
ENDIF
END DO
END DO
and add your SST change here. This will work if your met_em* files contain an SST field, or if your netCDF file global attribute contains FLAG_SST = 1.
DO j = jts, MIN(jde-1, jte)
DO i = its, MIN(ide-1, ite)
IF ((grid%landmask(i,j) .LT. 0.5) .AND. (flag_sst .EQ. 1) .AND. &
(grid%sst(i,j) .GT. 170.) .AND. (grid%sst(i,j) .LT. 400.)) THEN
grid%tsk(i,j) = grid%sst(i,j)
ENDIF
END DO
END DO
and add your SST change here. This will work if your met_em* files contain an SST field, or if your netCDF file global attribute contains FLAG_SST = 1.