Find out which starting point for the 45-degree guideline is used by your local Planning Office. As this is not set in stone, you could try and counter the 45-degree method by commissioning a daylight study. Use this to prove your intended design has low impact on your neighbours enjoyment of the property. It helps if you have no self-imposed deadlines to meet during the subsequent negotiations, which could be protracted, and expensive.
Because of the potential encroachment of light, obtaining planning for a 2-storey rear extension on a semi is generally more difficult that achieving planning for a typical 2-storey side extension. As always, it helps to be on good terms with your neighbour as any objections will make it harder to secure permission.
Assuming that the existing ground floor extension has been built legally, you can build the upper storey on top of the existing extension at the required distance from the shared boundary. This will require a beam to be installed from the rear wall of the house to the rear wall of the ground floor extension. Be aware that you will need to ensure the foundations are adequate for an additional storey.