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 MyQuickMac Neo is a trojan / virus, is that true?
MyQuickMac Neo is not a trojan or a virus. Sometimes antiviruses "think" that MyQuickMac Neo is a trojan. It happens because MyQuickMac Neo sorts your files. While sorting, MyQuickMac Neo moves and sometimes renames files. For antivirus programs, this behaviour is suspicous. So, they "think" that MyQuickMac Neo is a trojan.
You can always check it by yourself. For example, upload MyQuickMac Neo's executable to VirusTotal and read the detailed analysis. You will be able to see every single action that program does.
How MyQuickMac Neo solves name conflicts?
Suppose you have file "example.txt" in folder "Downloads" and "example.txt" in folder "Desktop". MyQuickMac Neo will rename one of the files. So, after sorting, there will be "example.txt" and "(1) example.txt".