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There are only two files that are essential to program the Full Frame Evaluation board 

PLD1.pof	(programming code for PLD1)
PLD2.pof	(programming code for PLD2)

Place these two files in a folder and select them as the files to be programmed with the Altera programmer 
(the order matters:  PLD1.pof first, PLD2.pof second) the code can then be programmed into the circuit board
via the JTAG interface connector. 

This essentially treats the PLD as a "Black Box" with no elaboration as to what is going on inside.

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Other Information:

For each PLD, the graphics descriptor file (.gdf) is the top level design.

The .gdf files contains one or more subdesigns that were created in text descriptor files (.tdf)
along with altera macrofunctions (tri-state buffers, 74165, DFF's....)

In order to place a subdesign block created in text, a symbol (.sym file:  block with inputs, outputs) is created to be 
placed in the graphics file and routed. 

These files together make up the overall design.
This design can be placed in any number of devices, with any number of pinout configurations.

The device used on the cicuit board must be selected and assigned.
The pinout used on the layout must be selected and pins assigned (really the compiler chooses the best fit and then
the pinout is back-annotated)

The design is then compiled and an altera configuration file (.acf) is created

The .acf file ties the design together and gives the following information:

1.) Which Altera device will be programmed
2.) The device pinout information, which pins the signals are assigned to
3.) The device layout, where inside the device the various logic blocks are assigned
4.) Any other design criteria the designer may have specified, (slew rate, optimize for speed or area, logic 
synthesis options, etc.)

The programming file (.pof) is also created during compilation.

These files (PLD1.gdf, Clocking.tdf, PLD1.acf, and PLD1.pof) are the important ones. (In fact, by having 
just the  .gdf, .tdf and .acf files one can compile the design and the .pof file will be created)

If the design is modified, the design then needs to be recompiled to update the .pof file (and the .acf file) 
to reflect the design changes.
