SPSite siteCollection = SPContext.Current.Site;
SPWeb mySite = SPContext.Current.Web;
SPListTemplateCollection listTemplates = //get a reference to my template here - this is not in the site collection, but in my project;
SPListTemplate listTemplate = listTemplates["Custom List Template"];

mySite.Lists.Add("Custom List", "A list created from a custom list template in my project", listTemplate);