I'm not sure I understand your question, so I'll restate what I understand in my own words. You have a program that looks for its configuration files in the same directory that the program is located in. For example, if you run
/home/human/ExecuteIt/FolderWithConfiaguration/Configuration1/executable, it looks for configuration files in
/home/human/ExecuteIt/FolderWithConfiaguration/Configuration1. You want to be able to run the program with different configurations, for example
/home/human/ExecuteIt/FolderWithConfiaguration/Configuration2. And you don't want to make multiple copies of the program.
You can make symbolic links to the executable in multiple directories, and make symbolic links to all the common files as well. For example, suppose the program requires three files: the executable
executable, a data file
data, and a configuration file
config. You have two different configurations, which you put in
/home/human/ExecuteIt/FolderWithConfiaguration/Configuration2/config. You have one copy of the executable and the data file, both in
/home/human/ExecuteIt/FolderWithConfiaguration/Configuration1/. And you make a symbolic link to
/home/human/ExecuteIt/FolderWithConfiaguration/Configuration1/executable in the directory
/home/human/ExecuteIt/FolderWithConfiaguration/Configuration2/, as well as a symbolic link to
ln -s ../Configuration1/executable ../Configuration1/data
The symbolic links tell the system to look for the real file in a different place. They don't contain any data themselves, so if you update the executable or the data in
Configuration1, this applies to all configuration; and there is only one copy of the files, so the additional configurations only require the disk space for the configuration file.
Most programs that behave this way will take the location of the executable into account when looking for data and configuration files. If yours follows the symbolic link, this method won't work. Instead, you can make a hard link. Hard links are multiple paths for the same files; all the hard links to a file are equivalent.
ln ../Configuration1/executable ../Configuration1/data
This makes it more difficult to update the files as you need to update the file designated by all the paths. Also, all the hard links to the same file have to be on the same filesystem.