I was like you new to rooting on my Galaxy Note 10.1, I did just like you for any app in multi window. Unfortunately the One app I use most, didn't work in the Multiwindow App. It wouldn't resize correctly. So I ended up going back to stock. I really didn't see the point in staying rooted as other than that app, I didn't know what else to do with Root. I don't really miss it, but I know there are some apps made just for root. I'm sure some other People who are more Use to Root on their devices can offer other suggestions for you. I will say that Rooting was very easy, it's just the pain of getting everything back to stock that I didn't like.