Updating caused 54 HTML code errors

I recently updated to 2.8.6 and it caused my site to receive 54 HTML errors. I check my sites coding every week and I previously only had 1 warning.
Now I need to change the coding to correct this, and I thought it would be a simple matter, but I can not figure out where to implement the change. I need to change it for the entire site so I am thinking that I will have to change it through my host Cpanel.
I have the corrected code already copied to a text file. Does anyone know for sure where I have to change this, before I go experimenting?
Thanks in advance.