what rom are you using? Depending on the ROM, you navigate to where it is with a file explorer, rename the stock to whatever, copy the animation .zip that you want to the same folder (renaming it what the stock was, exactly) and you're done.
I'm assuming you've downloaded a zip file from somewhere. Do not unzip it, just rename it to "bootanimation.zip" and place it in the directory that holds the original bootanimation.zip file. You can always make a backup of the original first.
This may depend on the rom, but usually you can put your new bootanimation.zip file in the /data/local/ directory, and the phone will use that without you having to disturb the original.
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