Click "Edit Settings" on one of your maps. From there click the tab "Icons".

Find the category that you want to use a custom icon to represent. Click on the image of the current icon for that category.

Click on the link "Browse all icons...". This will bring you to a page that will display all of the publicly available icons on the site. It might be worth exploring these, but if you can't find what you are looking for and still want to upload your own icon click on the "create your own icons" link.

Here you can upload your icon file. It works best if it is smaller than 40px by 40px and transparent, but it can be as large as 250px by 250px.

Once your file has uploaded it will display in the box to the left. Now you can drag the image around to line up with target and the shadow. All images are draggable. Once you have these set properly simply click "Save Custom Icon" at the borrom of the screen. This will save all the necessary values to position your icon correctly.