Notes

Go to options -> Overlay -> Deck Windows in the Hearthstone Deck Tracker.
Mark the “Player” check-mark. This will cause a window to pop up that shows your currently selected deck.
Click on the “Background” drop-down and select “Custom”.
In the “Custom hex” text box enter “#00ff00” (without quotes). This will set the background to pure green.
Now, open OBS, right click in “Sources” within whatever Scene you want to add this to and select “Window Capture”. Name it something along the lines of “Hearthstone Deck Tracker”.
Select the window called “Player”, Select “Inner Window”, Select “Sub-Region”, Click the “Select Region” button, drag down the top of the window so that you cut off the top of the window and press enter. (My settings are Position 0 29 and Size 230 560). Your settings may differ. If you didn’t cut off enough of the window, just come back here and adjust it down further.
Select “Use Color Key”. Double click on the color box. Select the third green down from the top. If you want exact settings, I have Hue 80 Sat 240 Lum 120 Red 0 Green 255 Blue 0. Click Ok. This ensures that all of the green background that we selected previously is hidden, similar to a green screen. Click Ok.
Now, just position the deck where you want it. I generally line it up where the deck naturally sits in the normal overlay.
NOTE: You must not minimize the window. Just leave it up normally in the background.