It may have been easier to split these into separate questions as there's a huge amount of detail you're asking for here. But here goes anyway!
1. - Firebug is your friend, it lets you see what styles are being used and edit them live to see what will happen.
2. You're not the only one using the OneUI. Personally I don't like it (hence this site using Blueprint CSS and our own custom css) but each to their own. It is very complex really so I would rely on using the XpagesFramework application from OpenNTF and not editing the UI elements of that template.
3. The dojo elements have their own styling as you've picked up. You can define your own theme and override all of the styles but again this is a lot of work. Overriding the defaults the way you're doing is really the way to go for simple changes.
4. Rule of thumb is that you should never use inline styling, always move that out to your stylesheet for maintenance reasons. Of course expediency sometimes takes over but generally you shouldn't be using inline.
5. Again Firebug is your friend.
6. It is the latter.