The custom info window can only have it's contents be modified, there is no options to control the info window itself. If you look in your google_javascript > wagmp_map_1 file you will see the custom info window text that you have applied in the wizard. You can add to it or modify it here if you would like but it will only affect what is seen inside of the existing info window.
As for using custom markers for certain locations this is also not an option from within the wizard. You could do something like this but it would be up to you to make the code customizations in the map file to get it switched out like this. Here is a link to a thread where someone has done something similar:
showthread.php?t=11733