The profiles listed above is great if you want pixel-accurate output. I found them independently while messing around the settings back last year.
However I get a big problem in that now the picture now “stretches” outside of the screen. So I either get scaling artifacts from the sampling size being inaccurate, or I get part of the screen missing. Line3x/4x would help with the scaling artefacts but my TV doesn’t work with them.
Also, for what game uses which resolution: most 3d games use 352 or 704, most Capcom games use 352 (it is closer to the arcade CPS2 resolution), most SNK games use 320 (closer to the arcade Neogeo resolution). For other 2d games it is a toss-up – they can use either.
I don’t know if any 3d game used 320 mode. I recall there was one or two, but I don’t remember which ones, I could be wrong.