What is "Machines manager"?
"Machines manager" is a special tool which helps you to view, ban and unban machines connected to unique license key. With it, you can ban certain machines from using your license.
My antivirus says that 4-Organizer Ultra is a trojan / virus, is that true?
4-Organizer Ultra is not a trojan or a virus. Sometimes antiviruses "think" that 4-Organizer Ultra is a trojan. It happens because 4-Organizer Ultra sorts your files. While sorting, 4-Organizer Ultra moves and sometimes renames files. For antivirus programs, this behaviour is suspicous. So, they "think" that 4-Organizer Ultra is a trojan.
You can always check it by yourself. For example, upload 4-Organizer Ultra's executable to VirusTotal and read the detailed analysis. You will be able to see every single action that program does.
How 4-Organizer Ultra solves name conflicts?
Suppose you have file "example.txt" in folder "Downloads" and "example.txt" in folder "Desktop". 4-Organizer Ultra will rename one of the files. So, after sorting, there will be "example.txt" and "(1) example.txt".