I'm a bit confused by the way you've worded this question.
I'm working on the prospect that you're wanting to have an animated menu to begin with, and if you select a particular button, it'll take you to a sub menu that has animated buttons of specific clips.
If you're wanting to have a specific section of the video playing as an overall background, then it's best to clip that section out of premiere pro and export it as a seperate file.
However, if you're referring to having little animated buttons showing specific clips from the whole video, this can be done from one timeline, simply using the chapter markers and pre designed or custom made menu's.
If you define the timeline/chapter markers on your video file when you bring it into Encore, when you go to the Timelines window (F11) I believe, this will show you your chapter markers in the bottom half of the window.
Create a new "Submenu" by selecting one from the library of predesigned styles, for example, PAL_Radiant Submenu, which gives you four boxes.
Simply select one of the timeline markers from the Timelines window, and drag it onto one of the four boxes on that screen and you should see your timeline image appear there. Repeat for each subsequent marker.
You can also simply drag a timeline marker onto your menu, and this will create a new button for you.
Once you have all your chapter markers on the menu, you need to go to the Properties window and click on the button that says "Animate Buttons" or words to that effect.
To test out your menu, select Render Motion Menu's from the FILE menu, and then preview it. Your individual chapter points have now turned into little animated buttons.
Hope that helps, let me know if there's anything else you're stuck on with this.
Other than multiple angles, coz Encore sucks for that and I hate it