Bootstrap is a hover pop-up, mostly used for read-only. This is more like a click pop-up both read-write. User can click, fill in a form and submit.

- If you want just drag and drop use jQuery UI.

- If you want to connect divs use jsPlumb.

- If you want flowcharts use jsPlumb + jQuery UI. jQuery to drag elements on to the diagram div and jsPlumb to connect them.

You can achieve almost every thing what ever is being done here. I have used it personally to create something very similar. jsPlumb is MIT License, so you don't have worry about any thing.