I'm not sure if you are familiar with the clipping functionality of the s-pen by default but you can do this easily without any third party applications out of the box. This is completely independent of multi window support though so I'm not sure how this function is relevant to your original post but in any case here's what you do for copying parts of the screen into evernote (or any other supported app):
- While viewing content you want to clip into another application take the s-pen and click and hold its button while the tip is away from the screen.
- Bring the tip of the s-pen to the screen and continue to hold its button down while drawing a marquee around the area you want to capture.
- Once your marquee is complete let go of the s-pen button. A bar at the bottom of the screen will appear that allows you to select an app to share your clip with.
- Prior to clicking an app to share your clip with you are allowed the opportunity to modify the marquee but your options are limited so be sure your marquee is large enough to capture what you want.
- Tap the app you want to share the clip with and that app should launch. For evernote the clip will be pasted into any note you have open for editing OR it will open a new blank note and paste the clip into it for you.
I use this function a lot with skitch to illustrate things to people and love it. It's the closest thing I can get to Snagit on my desktop.
Hope this helps.