Yes, phase them properly. It isn't hard, takes just a few minutes. At worst you swap two wires or flip a plug over.
I think the PH would trip it's breaker/not turn on if out of phase though. All my modern items shut off if out of phase at all, but I don't actually use a PH to know 100%.
Transformer breakers are not there to protect trains or accessories. They protect the supply. By chance they also protect the trains SOMEWHAT but not ideally.
Fuses should reflect amps expected to be used for the trains &acc. ,and/ or to protect the wire size used (like a long 18g wire hooked to a 15a ZW should be fused at just a few amps so the 18g CAN'T ever burn if directly shorted. (adding a second even lower amp fuse at the acc would be good second fuse location) (I ran 50+ fuses in a dune buggy so wires couldn't ever burn and strand me 50+miles from nowhere. Normally folks use 6 or 8 
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Breaker vs fuse... same thing really; thermal or electronic have different strengths and weaknesses. (folks forget these super fast electronic versions fail too, and sometimes they fail to stop the power flow. So a thermal backup is always suggested imo.)
Mind that there are fast blow and slow blow fuse options too; and fractional amp sizes too(4.5a, 4⅛a, etc.). This allows you to really dial in design safety if you apply knowledge of what blows when and why.
