Question

How do I specify additional connection nodes for custom shapes imported as SVG, by default only connection node is at the centre.

Answer 1

There are two ways to have edges connect at a position other than the node center:

1. Press and hold SHIFT, then start and and edge creation at the desired positions. (Both start and end position have to be inside nodes, though, otherwise the dragging the mouse will not be recognized as edge creation gesture.)
2. Click an existing edge, go to the properties view in yEd's lower right corner, and adjust "Source Port X", "Source Port Y", "Target Port X", and "Target Port Y" as desired. (With this approach it is possible to move theedge connection point outside the corresponding node.)

Answer 2

In more modern versions of yEd, there is a manual workaround.

You first connect the two shapes the usual way, letting the edge end go to the middle of your shape. Then, you click on the edge itself. The edge is highlighted and a small black rectangle is shown at the end. You can now click that black rectangle and drag it to where you want it.

The dragging is freehand, it doesn't snap to symbol boundaries or other features of the node. Unlike the two older workarounds from the other answer, it supports positioning the end outside of the symbol, while allowing you to chose the position visually, without having to enter numeric coordinates.