Help! I'm not advanced.

I need some help, if someone knows the area of custom themes. I am working on my church's website and one of my duties was to have a guy relocate the site from to
That went smoothly, but as I re entered that dashboard, it said that three themes needed updates so, without thinking, I updated them and the formatting of the site went screwy. Turns out there was custom theme work done and I overwrote it with the latest version of the stock themes.
I then had the host restore the domains directory to a restore directory. But copying the restored domains directory over top of the live domains directory did not fix the formatting issues but it did switch the site back from to
Does anyone know how I can successfully use this restore directory to fix the themes/layout?
Thanks much,