You do not need a dongle for 4D Organizer. The Smart Update also works for 4D Embroidery, 4D Embroidery Extra, and 4D Pro, and those do require dongles. The same routine is used for all.
You can add alignment marks to border designs in the customizing module (4D Embroidery) but not in Organizer. Your best bet (without additional software) is to print a template of your design and position it on your fabric for determiing the location of each repeat. You can line up the template with the design already stitched on your fabric. If you use vellum in your printer you will be able to see the design under the template.
Carol