Speaking from experience, I recently bought a used Apex, the first thing I would recommend doing is resetting the Apex to factory settings. To do this go into the main menu on the display and select System>Init memory>All. This will clear the memory and reset all settings to the factory defaults.
Then go ahead and setup the Apex so that each outlet you're using is named using a numbering system that corresponds to the outlet numbering on the EB8 or EB4. For example, use names like "returnpump_1" where the "1" denotes which outlet on the EB8 the pump is connected to, in this case the first outlet. This makes it easy to tell which outlet you're testing and in the future which outlet each piece of equipment is connected to.
Next test each outlet using a desk lamp or something else that is good for testing whether power is on or off. Next, to test the varspd outlets you'll either need an ethernet cable you can cut an end off of or some Cat5 or Cat6 cable that you can crimp an RJ45 onto. I don't remember which wires supply power, but if you simply search for "neptune apex varspd wiring" there are several diagrams that will come up on Google that can be used for finding out which wires need to be tested. Use a multimeter to check the voltage for each port's wires (2 ports per Cat5/6 or Ethernet cable). Check when the port is set to "off" and when it is set to "on" so that you can tell whether or not it turns on and off properly. It should read 0VDC when it's off and 10VDC when it's on.
Hope this helps!