This is the brief description for WRF/ROMS coupled model (dubbed SCOAR2) based on original SCOAR model (coupling RSM and ROMS).

More comprehensive model manual is provided here (thanks to Dr. Putrasahan)
The main structures are identical, so it is suggested
1) to learn both WRF (and WPS) and ROMS first
2) to get familiar with SCOAR shell scripts.

WRF
Some difference in WRF-ROMS is as follows.
WRF Pre-processing (WPS) and real.exe should be done before running WRF/ROMS.
The model does not do preprocessing during the integration. This is to save the CPU time to eliminate preprocessing time in the cluster.
1. In WPS, geogrid.exe, ungrid.exe, metgrid.exe should be done to produce the met.em*.nc files for the entire simulation period.
2. In WRFV3//test/em_real, then do real.exe to produce the wrfinput_d01, wrflowinpt_d01 and wrfbdy_d01.
For wrflowinp_d01, be sure to do the following in namelist.input.

&time_control
auxinput4_inname = "wrflowinp_d<domain>",
auxinput4_interval = 360,
io_form_auxinput4 = 2,

&physics
sst_update=1

If CF (coupling frequency) = 1day, WRF will run 24 hours with 3hourly outputs (WRF_OUTPUT_FREQUENCY=3 in main.sh).
In the coupler, daily averaged forcing and SST will be created.
If CF=6, WRF will run 6 hours (SST_FREQUENCY=6 in main.sh) with 3 hourly output. In this case, wrfout* file will have three time steps for each 6 hourly files (0th, 3rd and 6th hour). The coupler will use the values at the 2nd and 3rd time step.
WRF will restart every 24 hrs or 6 hrs depending on CF, producing wrfrst files. (this can be deleted later as they are large in size).

Other setups in namelist.input should follow the standard WRF manuals.
http://www.mmm.ucar.edu/wrf/users/docs/user_guide_V3/users_guide_chap5.htm

I used the WRF Domain Wizard.
http://www.wrfportal.org/DomainWizard.html

There are 5 sub-directory in the model
Lib, Model, Shell, Data, Run