Here's a quick map I've knocked up of the route of the East London Line extension through New Cross Gate.
I hope it gives a good idea of how everything fits together - the tracks along the top are the old ELL route (only the southbound will be in regular use), while the one along the bottom is the new connection. The background is a diagram of the under construction New Cross Gate depot taken from this planning application.
The new connection includes a flyover over the main line, the main span of which has been assembled alongside the line, as shown on the diagram. This bridge is far too heavy to moved by crane, so it's going to somehow be pushed into place using "self propelled vehicles". The planning application for the flyover is here, and includes some good diagrams and rationale.