So if you want to use MTPuTTY on Flash USB, you should put mtputty.xml in the program folder. Simply copy ptputty.exe to your USB flash drive and run it with /P parameter in order to create a configuration file in the same folder.
When you start MTPuTTY the next time, it will finds mtputty.xml in its folder and will use it and reads the config from it. But if you want to use your original mtputty.xml, just copy it to the flash drive (Note: you don't need to run MTPuTTY with /P parameter in this case).