I don't do layers, so I have no clue what advantages they might have. I just use different colors for different types of things (sights, food, shopping, infrastructure), all on the same layer.
To expand on what Mardee has said:
Search for something you want to mark on the map. Google may immediately show a pop-up (be sure it's what you're looking for), or multiple pins may appear (all the Coop supermarkets in the city, for example), in which case you need to select the right one. Being more specific with your initial search can help, such as including the name of the street where your destination is located. Alternatively, you can begin the process of flagging something by zooming way in on the map and touching the Google pin that's already there.
In the pop-up for the location you'll see Add to map. Click on that, and you'll see your plot point. It will be a blue pin. If you want to change the color or the icon, click on the first of the 5 icons to the right in the pop-up box (a tilted paint bucket), then choose a color and/or a new icon.
You can easily change the color and/or icon later, by touching the marker on the map and then the paint bucket.
If you want to change or add to the label for the plot point, click on the second icon in the pop-up box (a pencil). If you change the label for the plot point, you must click on Save afterward.
To create a plot point for a location you know but can't manage to specify so Google can identify it, get the right area of the map on the screen, click on the middle icon in the strip of seven just below the Search box (a pin), then click on the spot where you want the pin to show up. Create a name for the plot point and click on Save. To change the color or the icon, click on the paint bucket.
To my knowledge there is no way to specify the extent of the underlying map. Google seems to make its own decision about the base map, depending on the pins you create. You can work for a month on a map of Stockholm, then search for Eiffel, and you'll suddenly be looking at a map of Europe with a cluster of pins near the top (that would be Stockholm) and a prominent lime-green pin near the bottom (the Eiffel Tower). I often have a few pins for sights in surrounding towns on my maps for major cities. It just seems simpler to me to handle potential day trips that way than to have a separate map for each little town. Also, it's not a lot of fun to scroll through dozens of maps to find the right one.