MAME's folder structure

Hi all. I could use some help understanding the MAME linux (Ubuntu-based) folder structure better. In Windows, everything goes in the MAME folder, e.g. C:\MAME\. In contrast, in Linux Mint, I find the following:

• /usr/games [The MAME binary's location]
• ~/.mame ["Core Output" folders, i.e. cfg, diff, nvram, sta, ui, and the files ui.ini and mame.ini]
• /etc/mame [ini files, including another mame.ini]
• /usr/share/games/mame AND some are also in /usr/local/share/games/mame [Supporting folders, e.g. artwork, cheat, samples, etc.]

A couple questions:

1. Why are there two mame.ini files? Which one should I edit when I need to make changes?
2. The ui.ini file references folders that don't exist, but that I'd like to create, e.g. "marquees_directory {tab} marquees". In Windows, that means the the "marquees" folder goes in MAME's 'root' folder, i.e. C:\MAME\. There's no such MAME root folder for linux, so where is ui.ini looking for these folders?

The mame.ini and ui.ini files read like they're operating in a Windows environment, and I could really use help understanding how to interpret them for linux.