Upgrading with template override files

Thanks for all the great help out there! This should be an easy answer, but I seem to be confused.

I upgraded to v1.5.1 from v1.3.9 and everything seems to be going smoothly. I am currently loading my template override files into place. When I load them, how do I get those files to reflect any new coding in the 1.5.1 files. Do I have to go through and compare all of my old files to the new default files and merge them? How do I know if the code is something I changed vs. an updated code change?

I have a few MODS that affected base files, such as the COWOA MOD, but the majority are all using the template override system. I thought upgrading would be simple with the override system. Am I doing things correctly by comparing files before (1.3.9 original vs 1.3.9 modified), and then after (1.3.9 modified vs 1.5.1 original)??

Am I supposed to copy and paste changes from 1.3.9 modified files into new copies of 1.5.1 files??

Scenario:
a) you got a fresh copy of v1.3.9
b) you changed v1.3.9 by altering files to accomplish your personalized end result
c) now you got a fresh copy of v1.5.1
d) since v1.5.1 doesn't contain your own customizations, you need to get those customizations into the new files
e) so, you need to perform the same alterations in the v1.5.1 files.

In the case of override files, if the original versions of the files you copied to make your overrides have been changed between 139 and 151, then you'll need to replicate those changes in your override files too.