Depends on how the inputs are wired. If the Active versus passive are hooked up so they are isolated from each other internally, then no problem. If, it's like most cheap amps, it's the same input, but just a pad is on the active input, then a signal sent in one input can feed out to the other. Could be a problem for the Bass, or iPod
Best to use a small mixer, or an iPod interface designed to take your bass as an input to the iPod and feed this with the mixed sound to the amp.
AmpliTube iRig
Or the Peavey, or Alesis equivalent.