Cheesecake is a custard, so your very best indicator of doneness is temperature. There are a range of opinions, from about 150 F to 165 F / 65 C to 73 C, measured at the center of the pan, in the center of the layer.
If you don't have an instant read thermometer, generally, you want a thin knife to come out clean from the center; similarly, when the pan is shaken a bit, only the center should jiggle slightly. These indicators are not as good as temperature, so you will need to gain experiene to interpret them.
Once you are measuring properly, problems with the top of the cheesecake being done, but the inside being too unset may be mitigated by:
- Baking in a water bath (which you indicate you are already doing)
- Baking at a lower temperature (within reason; you indicate you are already baking at a fairly low temperature)
- Baking in a wider pan, so the cheesecake is more shallow
- Do not use convection
Since you area already using a bath and a low baking temperature, if you are still having problems once you start checking for doneness by temperature, I would suggest checking your oven's calibration with an oven thermometer to be sure it is not running hot.