Im curious why

Some more detail for the Arrow/Linear Tech's board can be found here: http://www.arrownac.com/mktg/resource_mag/may_2007/pdfs/resource-spr07.pdf (page 24-25 of document, 26-27 of pdf).

If you want to learn a little more about cyclone devices for battery powered applications, you may want to try to look at this board that linear tech and arrow put together:

I would also recommend using a switching supply. The advantages are twofold. To begin with, you will get more efficiency compared to a linear one and you will be able to power the system with draining batteries as long as the current drain requirements are met. You won't have to bother about having the battery voltage above linear regulators' drop out limit.

[My opinion] - You should definately use a switching power supply instead of a linear regulator for this battery powered application, even intial builds. Using a linear regulator, you waste the power from the supply voltage down to the regulated voltage. 5V down to 1.2 V puts you in the 25% efficient range. A switcher puts you at the 90% range. Consider an easy to use one such as

I've had a quick look at the LP3990 datasheet. Using a linear regulator is certainly a straightforward approach (which is why I used them on my prototype board) but it's not optimal as far as power consumption is concerned. Based on minimum input voltages recommended in the datasheet (2V for the 1.2V output regulator and 3.8V for the 3.3V output regulator) you're going to be wasting maybe 25% of your battery power. Depending on what your rechargeable cell voltage is, you might not be able to get these input voltages (e.g. you may have to use 2.4V and 4.8V in which case you'll be wasting even more power).

The Quartus II web-edition (free version) supports Cyclone III device family. See supported devices list at http://www.altera.com/products/software/products/quartus2web/features/sof-quarweb_features.html

Thanks, my research is pointing towards National Semiconductor LP3990s for the 1.2 and 3.3 volts I'd need to run a Cyclone II, not sure if the version of Quartus II I am running (free vers with cyclone II dev kit) will work with Cyclone III.

Just to prove you're not mad to try, look what turned up in my in-box today:

National Semi regulators sounds like linear regulators. Switchers are much better for power limited applications. I have power limited Altera designs, and I use the LTC3415 for core voltages for its efficiency. (You have to pay a little more attention to power supply noise.) Linear Tech also has an easier to use LTM series. Also easy to use is a series from MuRata that specifically targets FPGA voltages, MPD family.

Thanks, Im hoping these national seminconductor regulators will take care of that, I am beginning to suspect the external components for the regulators must be chosen carefully to do that, It needs a few capacitors, inductors and resistors that be soldered together several different ways. Hopefully I will have enough code written in a few weeks to start building designing a board, then building it.