At first I try to relate each area and the people that inhabit it with a certain language, religion, politics, cultural background etc.

For an example I have this country that is predominantly homogeneous in terms of racial/national diversity, like the majority is 80%. If they are a warlike, dominant people this means that all minorities will probably have their cultural heritage oppressed and thus, most of the places will have a similar morphology.

Another example will be a small and relatively young country which still does contain a majority of at least 65-70% but was conquered by another country at least 500 years ago and only recently gained it's independence. This means that other than the native majority deciding the names of places there will be many "residual" toponyms still named in the manner of the conquerors.

A third example would be a heterogeneous society which can have many different concepts of naming. Names can be determined as a cultural mix if the people live in harmony or different parts of the country will have different background for their respective toponyms.

After I decide the concept by which the places will be named I will look up different languages, both existing in the real world and from fantasy and start brewing names based on words from the said language.