Hello Cyril,
"Main directions 1&2" corresponds to the directions of the 2 modes of the spectrum (typically, mode 1: swell and mode 2: wind sea, but it can be something else according to your site). "Initial" means that theses directions will be applied for all the spectra of your mesh, at the first time step only. "Boundary" refers only to the spectra located on your liquid boundaries, but for every time steps.
The number of direction refers to the discretization of your spectra in direction. The range [0 360°] will be split in as number of directions as you ask for with this keyword.
I don't really know what is the best way to your case, it depends on the characteristics of the sea states in your area, the availability of data, what you really want to represent.. You need first to have a good knowledge of the sea states in your region (offshore incoming swell(s), locally-generated wind sea, influence of tide near the coast...). If spectra measurements are available, you can look at their shapes (1 or 2 modes) and see if TMA or Jonswap (maybe more frequently used) are in agreement and which parametrisation is suited. But these parametric spectra only are theoretical representation of a real sea state.
You can also check the availability of numerical databases offshore your area that can be used on your model boundaries.
Once your boundary conditions chosen, a good parametrisation of the source terms is really important and have a significant influence on your coastal results.
I hope it helps.
Laurent