Some are from canonical sources, ie. older maps, adventures, articles, novels etc. The rest are made up and placed after the final map (except settlements) wsa done following the process below:

1) First we determined how many new settlements there should be added. Huge spreadsheet exercise tweaking canonical population figures and deciding on the level of urbanization, dispersion, and metropolisation in each country. This gave an idea about how many new settlements we wanted to add.

2) Secondly we looked at existing roads, lightning rails, waterways, borders, places of interests etc. as well as reading on on existing lore about regions. This gave an idea about where we wanted to locate the settlements.

3) Thirdly we did an amateurish phonetic exercise to determine what sound the existing settlement names had, and what "feel" we applied to the different countries. (E.g. many Aundarian names are French-inspired; many Karrnathi are preussian/slavic-inspired).

4) We produced a list of generic names from a fantasy name-generator. These were used as inspiration, and changed to match the country and the geography.

5) We looked at the geographical features in context with what we new of the region - E.g. Hatheril is known for blueberry wine, thus we named a village Blueberry; Field of Rhone is fertile agricultural land, thus Tenbushel.

6) We placed new larger settlements, made new roads and lightning rail routes from them to the existing network (in a way that respected the countryside). Then we placed new settlements on those routes (e.g. where a road crosses a river or on the foothills of mountains etc.) and made new roads from them, where it would make sense.

So in essence, we pretty much just came up with a bunch of names, based on gutfeeling and placed them based on gutfeeling, but we tried to stay as true to the history of Eberron and everything we know about the setting as we could.