This forum helped me a lot. So here's what I just did. BTW I used a R4 and f2a (not ultra)
First off I downloaded fas1 (http://code.google.com/p/fas1/).
Second I got the legend of zelda a link to the past/four swords.gba (actually had this one already)
Third i got GBA tool Advance (http://www.no-intro.org/tools.htm)
Now I used GBATA to patch zelda to SRAM because it uses EEPROM for saves and the f2a doens't have that.
At last I followed the instructions from fas1 (make a GBA map on your R4 or fas1 doens't recognise it)
First off I downloaded fas1 (http://code.google.com/p/fas1/).
PLEASE NOTE: THIS DOES NOT WORK WITH FLASH2ADVANCE (F2A) CARTRIDGES The library for flashing a f2a cart is in ucon64, and can be found here: http://www.koders.com/c/fidC5AEE87302951FF4854331F1B326B3ADEEC05D48.aspx
I tried yesterday on my Flash Advance Card Xtreme 64, it did work but it erased all the GB and GBC games I had for my GB bridge.that homebrew was written by smiths, of AKAIO fame.
it should not support the flash2advance:
so i'm rather curious. i wish i had asked the OP in 2008 if they were sure that they had a flash2advance, because this flashing software has never worked with my f2a.
-another world