All three terms you mention are clearly understandable:
- Properly configured
There are other similar terms you could perhaps use, but it depends on the context and the message you are trying to convey. Are you talking about something like an engine that may only have one correct way it should calibrated? Or are you talking about something like a piece of software that has configuration options akin to preferences? If you are talking about preferences then I don't think there is really a definite right and wrong way for something to be configured.
To me, the terms you mention carry these meanings or inferences:
Configured - that someone has gone through configuration options and either verified them, or perhaps made some changes. In the case of something that has only one correct calibration, this might mean it is operating correctly, or optimally. But in the case of something with configuration preferences, it doesn't imply right or wrong.
Misconfigured - implies that a mistake has been made, perhaps one that prevents or hampers operation.
Properly configured - this implies to me that something has been configured optimally, and that there may be gradations of configuration where whatever "it" is may work, but perhaps not the best way.
You might also want to consider:
"Correctly configured" - if you want to indicate that there is just one right way to be configured.
"Poorly configured" - not the exact opposite of "correctly configured". To me this would imply that something will still work, but not optimally.