I've done some research on this... here is a link to the routines that can handle program flow such as that in the neogeo manual.
NeoGeo User Sub Routines
Just by changing the line in the crt0_cart.s file you can get the NEO-GEO logo to animate. The sound will probably play also...
_EYE_CATCHER = 0x00 /*;eye catcher (0-common 1-custom 2-off)*/
I did a quick try with my current project and it animated just like the real logo, but the graphic was wrong and sound was missing. This means that graphics and sound need to be in the correct place, which is most likely why it is turned off.
Here is a link on the
Eyecatcher