You should be able to reference the control after adding in a tag prefix.
<%@ Register TagPrefix="custom" Namespace="SitefinityWebApp.Custom" Assembly="SitefinityWebApp" %>
You would just need to change the Namespace value to the Namespace of your User Control. Then in the control element, change out "controlname" with the name of your user control class. And finally, you would change add in your custom properties as you would in a control designer.