For the second question I would recommend using hotspots to reveal the sub processes. You could do this by having the layer toggle on and off or by directing to another page using the hotspot. For information on how to accomplish this, see this article: Actions (Links) and Hotspots
The first question is more of a question on how you prefer to diagram. Personally I would have an output from processes A and C that I would have as inputs for process D. To keep them visually connected I would have different colors for the outputs/inputs for A and C and I would consider using the Hotspot feature to link them to the page the other process is on. Unless it is on the same page in which case I would probably have it toggle a layer with a line connecting the previous process.