If the pin-out spreadsheet doesn't make sense to you, maybe the pin-out information in Quartus will.
If you haven't started your design project yet, you can create a project for a dummy design to look at the device in the Quartus GUI. Without any design file at all, you can use "Assignments --> Pin Planner" to get a graphical view of the currently selected device showing the pin-out.
You sound like you want to do a design that could be programmed into either an EP2S90 or an EP2S130. Select one of the devices in the Quartus project. Then at "Assignments --> Device --> Migration Devices", select the second device. Quartus will then let you use only the I/O pins that are available for both devices. With the Pin Planner active, "View --> Pin Migration View" will list the pins for both devices side by side. This might be easier than comparing spreadsheets.
