Filezilla is OK... we use WS FTP Pro from Ipswitch, as it is more sophistcated and secure. Considering that we do an average of 3 full installs every month, and have done so at that rate going on 7 years now, using a good FTP program is essential. It's also better at error capturing and reporting, as well as choosing the correct transport type (ascii or binary)
We have loaded many hundreds (perhaps thousands) of templates and maybe even more modules and add-ons, and the "rules" are pretty much the same for all of them.
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Go through the README in the add-on, after unzipping it on a local machine.
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Where folders are to be renamed, do so.
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Where files are to be "merged", do so with a program like winmerge.
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where stuff is overwritten, make a full backup of the original.
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Then... you are ready to FTP.
Filezilla / WS FTP ... will have TWO PANES open (usually the LEFT one is the LOCAL machine and the RIGHT one is the REMOTE server).
Navigate on your LOCAL machine to the CORE FOLDERS involved in the module... in many cases, this is the same directory level as zencart CORE or ROOT level.
For templates, its almost always just an** includes **folder, with possibly a READ ME file. In rare instances it could have OTHER folders.
Inside that INCLUDES folder are likely to be three or four more folders (extra_datafiles, languages, modules, templates).
DON'T drill down into them... stay at the "includes" level.
NOW... IN THE RIGHT PANE OF YOUR FTP... navigate to your zencart ROOT installation. You need to be at the level where you ALSO SEE an "includes" folder.
Now... drag the "includes" folder in the left frame of your FTP to the "includes" folder in the right frame.
In some FTP programs you need to HIGHLIGHT the includes folder in the left frame, and click a little right-pointing arrow, showing the direction the transfer is to happen.
It really can't be any easier than that.