Hi Alberto,
If you only want to prescribe sea levels at open boundaries, you are right, you have to use the 5 4 4 code in the boundary conditions file.
If you use the default option for OPTION FOR LIQUID BOUNDARIES (= 1), sea levels are prescribed as a Dirichlet condition, and that may lead to a not well posed problem.
If you use the Thompson conditions, the boundary conditions may be more physical (in particular for entering waves). Nevertheless, it is more CPU time consuming, and is a bit more unstable: some spurious oscillations may appear, that is why using a FREE SURFACE GRADIENT COMPATIBILITY coefficient lower than 0.9 (or even lower) may be necessary.
Hope this helps,
Chi-Tuan