@kaneo1234, As Michael says,
Hype is just a development environment. Your project is exported in several ways. One being a html file and it's associated javascript file and the resources (video, images, etc). These can then be inserted into most existing websites.
In short, yes. If you search the forum you will find many posts on syncing animations with video. You can use some of the techniques on your own project. For example, this is a post I did a little while ago about syncing video with animations in Hype.
This is a little difficult to answer as it depends on how comfortable you are with Javascript. If you are ok at coding your own small scripts then it shouldn't be too difficult. If you have never done any coding then it will probably be more difficult. 
It really does depend.
There is no "branding" unless you want there to be. As Michael says, there is an option to turn off / on the "Built with Hype" on export.
D