When perl scripts use relative paths to find files, this path is usually (unless the author did some magic with Cwd or the like) relative to the current working directory, not to the directory in which the script lives.

So probably all you have to do is to create your directory, move the scripts to that dir, but run it from the same directory as before (or chdir to that directory in your wrapper script prior to executing script 1).

I hope I understood what you asked. If not, try to explain a bit more, and tell us what your actual problem is (creating a directory isn't complicated...).