Hi,
The default boot flow of the default firmware is (indirectly) documented in the official 1.0 BSP build guide. Up to 1.0 this boot flow has never changed. Note: if you are using non-official firmwares then anything else is possible. Now going back to the default firmware here is how it works:
1. EDKII is pre-configured to chainload the GRUB instance in the SPI flash. This can be changed by messing with EFI variables but you typically don't need to do that because there is much simpler:
2. GRUB then searches for a boot/grub/grub.conf located on the first partition of the first mass storage device (USB or SD). If it finds this config file then it boots whatever is configured in it. Providing this config file on your SD card at this well-known location is what you need to do and nothing else.
3. if this very specific boot/grub/grub.conf file is not found, then GRUB falls back on the grub config file embedded in the SPI flash, which by default boots Linux in the SPI flash.
Note: you cannot boot any "vanilla" Linux kernel because it won't support Quark yet; you can only boot Linux kernels compiled with specific Quark patches.
GRUB does not care about partitions being marked as bootable or any other thing like that; it only looks for the config file. Don't trust everything you read on the internet :-) Instead focus on the official BSP build guide. Sergey's blog is also very good and very accurate:
Intel Galileo - Building Linux Image - Malinov Family Web Presence