Whichever you choose it will all work with Pyblish. I'm saying this because Pyblish was meant to be customizable, and it does that very well.
This will be all up to your specific Integrator. That'll be the plug-in that positions your file into your own structure. Pyblish by itself will not block you to do anything you want nor does it make any of such assumptions. Pyblish says it's your pipeline and pyblish supports that. In its core it's purely a framework to help you publish easily, consistently, safely and exactly how you want in the end, according to your own implementation.
Regarding choosing a convention for naming I'm not sure what you're going for. Is the username after the extension? That'd be odd. I'd recommend avoiding spaces, and underscore or dots are both great separators. Some tools might get confused with the dot splitting to extension, but most (good) tools shouldn't. Nevertheless I'd recommend
_ as a good common separator.
I have to admit that your question is somewhat unclear. Specifically what kind of problems are you expecting? And why do you think they would occur?