I'm working on a template that was given to me. I don't have any expierence with after effects, this is my first project... But when I duplicate one scene and paste in the new duplications. Changes that I make to the new scene also changes the original scene that I duplicated... HELP! its gotta be something simple...
After Effects uses nested compositions, or pre-comps, to stack elements from many timelines )compositions) into others. It's a very powerful feature that allows very easy cascading changes to complex jobs.
Without being able to see your project, it sounds like you are using nested elements and not properly duplicating or replacing those elements. It's essential to duplicate comps properly and replace them within your comps in the correct way. Template projects often have very deeply nested structures, with many levels of precomposing needed to be duplicated.
I use this script all the time, which automatically duplicates everything within a complex nest of comps:
Unless you post specifics, with screen grabs and/or project files, it's hard to diagnose anything much more than that.
After Effects is a complex tool which requires plenty of practice and learning. I strongly suggest you start at the beginning: