OrCad Library missing pins?

I am working with Allegro Design Entry CIS to do some schematic work with the cyclone III (EP3C40.OLB ) library. I am using the 240-pin QFP model (EP3CQ240) from the library but have noticed that several pins are not shown in the schematic or the model viewer.

I did a count of the pins shown and only 132 show up out of 240. Mostly what are shown are the GND/GNDA, VCC_INT, VCCA_PLL, VCC_IO, and VREF pins. When I was using the pin planner in Quartus II, I chose a few pins that are labeled ROW IO, DIFFIO and some more to use as input pins.

Should I only be using the VREF pins for inputs? I require about 60 input pins, but there are only so many VREF pins available for user I/O (~20ish). How can I represent all these inputs in the schematic?

I have attached a snapshot of my work environment using the Allegro model to give a better idea of what I'm looking at here. Also I have attached a snapshot of a pin I was hoping to use as an input selected from the pin planner of Quartus II. Finally another snapshot of my schematic so far.

The whole reason why I am making this schematic is to send it off to a PCB designer for a simple fan-out design of the fpga so I can start configuring the device. Maybe there is a better way to do this? Essentially I just want to describe to the the designer that I require different power islands (VCCIO, VCCINT and VCCA_PLL are separate), and a few pull up resistors, caps and schottky diodes, and a 10-pin male header for the board design.

Any help or feedback is much appreciated.. This seems like it should be the most basic thing to figure out, but I'm still a noob to altera :p