Hello Nayef,
As written in the TELEMAC-2D user manual, for OPTION FOR WIND = 3 (wind variable in time and space, but this can be generalised for other atmospheric variables), you have to implement yourself the treatment, e.g. in the METEO subroutine.
So, for your 1st question, you can do what you want, 1 or 2 files, but you have to manage how to read the values in 1 or 2 files.
You can have a look at the $HOMETEL/examples/telemac2d/wind_txy example which gives you an example to do with wind, but you may already have used it.
Hope this helps,
Chi-Tuan