I often run into the situation that I need to quantize something like mixed 16ths and 16th triplets. In that case, you have to quantize to the greatest common tuplet value, 32nd triplets. But with smaller quantize resolutions, you're more likely to run into problems if your timing was loose or everything was late, causing some notes to move the wrong direction.
At that point you usually need to use some combination of manual tightening and quantizing sections or maybe even creating a clip to use as a groove-quantize reference. At some point, though, you have to carefully analyze what's going on musically so that you understand where you need to get to.
I'll usually start be setting a snap value in the PRV, and seeing whether everything is close to a gridline. If not, I know I need to go lower. When I get to where it looks good, and I'm at a value that makes musical sense, I'll quantize to that resolution (usually only to 50-75% strength), and have a listen. If only a handful of notes moved the wrong way, I'll Undo, see where they should have gone, and drag them a little closer to the target before re-quantizing.
Undo is your friend here. Another trick I use is to repeatedly alternate undo/redo as I scroll through the track, watching how things move in the PRV to help find the trouble spots that need special attention. If something moves a lot further than everything around it, either the resolution is too high or it needs a manual timing adjustment.
If you have to resort to quantizing sections, I recommend working 4-8 bars at a time, and using Save As (or Save a Copy) to save versions like "My Song - Q'd Thru 32". This way you can easily revert if you find later that you really hosed something halfway through.