It is typically recommended to flash banks 1 and 2 with your mod BIOS of choice (which I would recommend X2 5035) and banks 3 and 4 with FlashBIOS. Remember to use the mod BIOS and FlashBIOS that are compatible with your box, 1.6 and 1.6b boxes have different needs than 1.0-1.5 boxes.
It is recommended to have the mod BIOS at the front of the chip since FlashBIOS always starts writing from the beginning of the chip. So if you later use FlashBIOS to put a new 512KB BIOS on your chip and something is wrong (ex., a 1.6 flavor BIOS on a 1.0 Xbox) it doesn't overwrite FlashBIOS. You can still flash over that first 512KB to correct your error.