Adding cities in the map editor is one of the few things I CAN do with it. In the upper right corner, at the end of the line of terrain icons, is a little city. Click on a square with the 1x1 cursor, then click on the city icon, then hold Shift and left-click. Dialog box will ask you what civilization. Pick one. Pouf! City, named Babylonians, for example.

Death -- the above is what I was referring to, not start spots.

There is not much to do with the map editor for what you are asking. Once you have the map you want, determine the starting locations you want, but this isn't really important since you create the cities during the game anyways. So really the only thing you need to do with the map editor is create the terrain you want (although this can be done in the game too, but more slowly)

Start a new game using premade world. select the world you want and be sure to start as a white civilization (russians etc.). This will ensure the ai doesn't build cities where you don't want cities. Then you can activate cheat menu and click on reveal entire map. Now right click to move the square cursor to where you want a city and then go to create unit under cheat menu. activate settler by clicking on him and then create city. To do other civs, go to change human player and select the civ. then create cities for that civilization.

I normally create all the cities I want first. Examine the map to make sure. Then I begin modifying using edit city and using the cheat command when inside the city screen. Military units I create inside the cities using the city screen and cheat build (although this assigns that city for support). If you want unit with none as support you have to use the create unit under cheat menu.

one more thing when you want to save you can save as scenario, but you can also save it as a regular game if you are unfinished. and then pick up where you left off (just click on load game- although cheat menu will be activated which you want) without having to actually start a new scenario to get to your scenario. So i only save as scenario when I am finished.

sorry if that is repeating what you know, just wasn't 100% sure what you were asking.

There was a guide to creating scenarios around here you might want to look for. Extremely helpful to me especially since it told me how to get the correct year to display properly with 0 turns elapsed.