If you make your UserControl inherit from SiteModuleControl the you have intrinsic moduleId and ModuleGuid, you can store these in your custom table and use them to lookup instance specific content from your feature. ModuleGuid is like an alternate primary key. We join on moduleid for performance but moduleGuid is handy for things like if you want to integrate the ContentRating system in your feature, you can store ratings with your moduleguid and retrieve ratings with the same. So it's best to store both moduleid and moduleguid in your custom table.
Study how existing features work will answer most questions about how to implement your own.
Hope it helps,