First of all welcome to the forum.
The RSII Beta, RSII Ready and RSII_Public folders are just different copies of my RTW install I have ready for various things. I installed RSII (public released version) into RSII_Public so I know what was in there. It's simply a copy of my 'Rome - Total War' folder.
We do that to ensure that there is a clean working copy of RTW on the PC - so if I mess up an install I can just delete the folder the mod was in and then start again. This approach does mean that I don't have to uninstall and reinstall RTW again.
When you see the message it usually means that the install did not work or you are trying to use an exe that is not in your install.
At the end of the install process your folder contents should look like the following (you may not have the RTW Alexander exe):