I know what you mean about having neat organization.
Probably if you were seriously going to generate a large amount of content under a specific tag such as yuri, then a separate yuri thread would be the way to go, but probably still under the members manga art board.
maybe a "members themed content" child board under members manga art would work for those that wanted to separate their work, or put both the yuri and yaoi as child boards of members manga art as well. although if you take MR as a guide, we just post everything in the same thread.
if you just randomly posted stuff and some was yuri or yaoi then one thread for everything and just put spoiler warnings on them.
although I won't be going that route, a hentai board with individual member threads for manga creations would also be appropriate, rather than just one thread with everyone posting.
again, its down to how many threads you want to manage, and how specific you want each one to be. it would be great if the picture posting was more like deviantart and we could tag individual images, make galleries etc, but that's a serious thing to add, and it already exists in deviantart and other places.