Just suggestions, no hard-and-fast rules:
1). Which hole depends how you are going to finish the pipe. If you use an eductor you can aim it down the centre for flow or aim it at the front or back pane to create a gyre flow.
2). Put unions and shutoffs where you can reach them quickly and easily, especially in an emergency. That will be determined by placement of the tank in the room, i.e. where the walls are, what sort of cabinetry you have, if you have a separate fish room, etc. Just make sure you can get at them quickly when things go wrong (and they will, sooner or later).
3). You can easily examine the plumbing set-ups of the many tanks here. Basically you want a flow from one end to the other, going from highest baffles dropping down to lowest baffles. You didn't say whether you will use filter socks, but these would be in the first section of the sump that your drain from the tank would go to. Then down to the next sump section for the protein skimmer depending on the water height yours prefers to work at. Then a section for your dosing and filtering reactors. Then back to the return pump section last. In between you need to find a place to put your heaters, any monitoring probes you choose to use, and a sensor for your automatic top-off system, if any.
Which elements of the above you choose to use is entirely up to you. If you're not familiar with this stuff you might also want to consider getting the
Mr. Saltwater Tank ebooks for pictures and explanations. No forum or magazine article can provide enough detail for the amount of information you have just asked for.
Dave.M