"zencart install program"?
There are two parts to Zen Cart: a) all the PHP,etc files and b) the database.
The only "install program" would be "zc_install", which mainly takes care of setting up initial database contents, by asking you a lot of questions. But you can only do that after you've uploaded all the files to your server, using FTP. And since the FTP part is up to you, you can control which folder you upload everything into.
So in that respect the "zencart install program" has nothing to do with what folder your store runs from.
And, yes, there are complete installation instructions in the /docs/ folder of your Zen Cart files. There are some basic instructions in the .html files, and there are detailed instructions in the ImplementationGuide.pdf file.
Your posts sound like this is the first time you've set up a website, and yet you've been posting here for a few years. Why all the sudden confusion?
Or is there a lot more going on behind the scenes which you're not sharing?
.
Zen Cart - putting the dream of business ownership within reach of anyone!
Donate to: DrByte directly or to the Zen Cart team as a whole
Remember: Any code suggestions you see here are merely suggestions. You assume full responsibility for your use of any such suggestions, including any impact ANY alterations you make to your site may have on your PCI compliance.
Furthermore, any advice you see here about PCI matters is merely an opinion, and should not be relied upon as "official". Official PCI information should be obtained from the PCI Security Council directly or from one of their authorized Assessors.