Steve,
That's good news-- the Atlas 1056B01 is an excellent remote and it is possible to make it work with the SH-AC500D.  However, it does require doing a little more work than just assigning a setup code.  You'll need to enter a 5 digit EFC for each function.

First decide which buttons you want to use for the functions.  You already have the receiver set up on the Audio device button.  You may want to redefine some of the buttons in Audio mode so that the processor will respond to them instead of the receiver.  Or perhaps you'll want to use a different device button (I'll use VCR as an example) for the processor. Then:

A) Redefine the VCR button to change its type from Video to Audio.  (Skip this step if you're going to use the Audio button for both the receiver and processor.)
1) Press Setup until 2 blinks
2) Enter 992  (should see 2 blinks)
3) Press Audio
4) Press VCR  (should see 2 blinks)

B) Assign Setup code 1308 to VCR  (Skip this step if you're going to use the Audio button for both the receiver and processor.)
1) Press Setup until 2 blinks
2) Enter 1308  (should see 2 blinks.  If it doesn't blink twice, then step A didn't work)

C) Assign EFCs for each function to the buttons of your choosing.  Note that you can't assign EFCs to the device buttons, Setup, or Master Power.
1) Press Setup until 2 blinks
2) Enter 994  (should see 2 blinks)
3) Press Setup (don't hold it)
4) Enter the 5 digit EFC  (44862 for Vol+)
5) Press the button which should send this command (e.g. the Volume up button)  You should see 2 blinks.

Repeat step C for each of the functions below. 

volume +    44862
volume -    44990
balance left    44894
balance right    45022
Surround Up    44814
Surround Down    44942
Dig Space On    44854
EQ On/Flat    44854
EQ SFP    44854
Snd Field Press    44854
Space    44982
muting    44918
Help    44966
power    44934
power on    44870
power off    44998
Dig Space Pr    44923
EQ SFP    44923
Preset-Fix/Ur    44923
level +    44827
level -    44955
Line    44843
digital 1    60779
digital 2    60907
digital 3    60683
Vid CD Power    60819
dimmer    60883
Aux/CD    60771
TV    60675
VCR 1    60739
Game/VCR2    60767
dr comp    60719
Cinema Re-EQ    60847
surround    60911
DTS    60687
stereo    60751
AC-3    60879
Dolby Pro Logic    60695
Channel Select    60903
Up    60679
Down    60807
level    60743
delay    60871
delay +    60713
EQ Effect Up    60713
delay -    60841
EQ Effect Down    60841
Center Up    60745
Center Down    60873
test    60757

Edited to include more functions.