Yes, for APEX series devices you can clock negative-edge triggered registers in the IOE from a PLL, but all IOE registers must be clocked with the same polarity from a given PLL output. Specifically, for any given PLL output, you can only clock either all positive-edge triggered IOE registers or all negative-edge triggered IOE registers. See Figure 1.
Figure 1. PLL IOE Clocking
Therefore, if you want to clock some IOEs on the positive edge and some on the negative edge, you would need to use one PLL output for each.
If you are getting the error "The <PLL port name> port of <PLL cell name> cannot feed IO cells both positively and negatively", then you have mixed polarity clocks for IOE registers (input and output registers) from a single PLL output.