Hi Laura,
If you only want to consider wave influence on sediment transport, I think the simplest way is to program into sisyphe by the way of the subroutine condim_sisyphe.f that does nothing by default. A simple example with no waves is presented in the subroutine, with comments. You have to program something here for reading your wave data from the "hydrodynamic file" (SISHYD) or your "wave file" (SISCOU), at the right time step corresponding to your t2d/sis simulation, and eventually interpolate them between 2 time steps (depending on how often you did graphical printouts from your previous t2d/tom simulation). Your wave data have to be stored in HW, TW, THETAW arrays, and you needn't to manage depth and currents, as t2d will do it for you.
In this way, "clandestine variables" and "wave driven currents" are useless and not taken into account.
However, If you also want to consider "wave driven currents", you have to provide the wave file (toma_BCG_v711_mercator_sim9.slf) to t2d steering file (thanks to the "binary data file 1" for instance, and by activation of "wave driven currents"), and to program the reading of your wave data to provide the driving forces FX, FY to the subroutine prosou.f to fill the FXWAVE and FYWAVE arrays at the right time step, in order to t2d can compute wave driven currents.
If you choose this solution, maybe you can directly access the wave data (Hs, Tp, dir) into sisyphe.F (without providing them by the "hydrodynamic file" or "wave file") and put them in the HW, TW, THETAW arrays.
If you also look at the morphological changes, Costas is right, you have to be careful with the validity of wave results, as long as the bottom changes are not too high.
Moreover, I'm not really sure that you're going to save too much time by doing a first computation t2d/tom (long) and then a t2d/sis with results of tom (fast). The 3-way coupling may be simpler for you and probably not much longer.
Regards,
Laurent