Electronic – How to connect two different DC power sources together

There's no way I'm reading all that PDF to find out what you need the power supplies to do. Please summarize it for those of us that don't need to know all the details of your project just to advise you on one part of it.

However, that said, here's my immediate thoughts:

1. The only way to properly isolate a power output from its source (and hence from any other power output on the same source) is with a transformer.

2. The only way to use a transformer is with AC.

So, if you can generate an AC wave form with enough current capacity to do what you require, you can use that to drive a transformer, which you can then rectify/smooth/etc the output of. This could be a multi-tap transformer to give you multiple outputs, or it could be a two single tap ones.

Of course, if you don't require 100% isolation, then there are other options. Two switched-mode power circuits running off one feed will give a certain level of isolation between the two circuits. It all depends if you require complete isolation, or just enough such that over-current on one output can't cause a voltage drop on the other output.

If you have isolated circuits you can always choose 1 reference point on each circuit to connect to the other. Only one. In most case that will be the grounds.

Both 5 V supplies are isolated from each other through transformers, then you can safely connect their grounds together.