I'm replacing a Little Giant pump that's wired into my HVAC as well as plugged into an outlet. Re the two low voltage wires on the pump, both are black. One is hooked to a yellow, the other to a red. I have 2 questions... Does it atter if the colors are reversed, AND, if I decid not to hook up the safety switch, do I leave the Y and R disconnectec or do U join them together? I belueve the manual says the switch is NO(normally open?)

Wires can be hooked to either or, just making and breaking contact

That switch is a NC (Normally Closed) switch. It's there to shut down the A/C if the condensate pump gets too full. If the pump is in an area where overflow could cause damage, I suggest connecting the switch.