What is your study period? I suppose that your period covers the time when the data is changed, please let me know if I am wrong.
For the soil levels, since WRF only needs soil information at the initial time, you can specify the information based on the data at the initial time of your study.
For upper air data, you need the same vertical levels at all the times. In this case, please take advantage of the WPS utility program mod_levs.exe, which can process the input data and make them to be located at the same levels. Please take a look at:
https://www2.mmm.ucar.edu/wrf/users/docs/user_guide_v4/v4.3/users_guide_chap3.html#_WPS_Utility_Programs