Are you using an ftp program to upload the files to the server?
Most (probably all) ftp programs will effectively merge the two includes folders. In other words they will add the new files to the existing folder.
So, that's the simple part of the answer. However, if the new files contain a file that already exists in the installation, then the ftp program will overwrite the existing file (usually with a warning). If you have not made any changes to the file that is being overwriten then that is not a problem. I suspect that if this is your first add-on then you don't have that problem. As you go on and install more add-ons you just need to check that the new add-on is not altering a file that has previously been edited by yourself or by a previous add-on.
On a slightly different note it is worth understanding the override system that Zen Cart uses. I am sure there is a tutorial about it or search this forum for more information.
And remember - if you have a back up of the installation before you install the add-on then you can always just revert to the back up! BACKING UP IS GOOD and will save you some tears.