How can I use Multiple mods that use same files?

So Ideally, I want to use a bunch of mods. However, some of the mods upload the same file but use different coding in each to make their mod work.

In one of the readme.txt, it stated:

"If you, or any mods that you have installed, have changed any of these files (or over-ridden the last one), then you will need to merge any changes into the relevant file."

Does anyone suggest a good way to merge two mod files into one?? or get around this? I feel it is impossible trying to go line through line trying to find the differences between the two files. I'm stumped!

You can use a program like Winmerge or (my choice) Compare It! to compare the versions of the files and insert the necessary parts to make the other mod work.

I'm afraid the manual method is the only way to accomplish this, so I think it's best to only install mods you're sure you can't live without.