You can't mess up her events wiht your choice. Have you perhaps not found Maria at The Drunken Cave in Begus yet?
Else, a step by step guide of main character events can be found in the walkthrough.
If you had the event with Maria at the Drunken Cave, you need to go to the Ironholm prison next, where you need the help of the ghost girl Shey from Old Ashton.
Once those events are also done, you can find Maria for the next step at the top left of Havaria port.
For Chiyo, you might need to advance the main story first, or the events in Amagal.