MAKERbuino is using a special bootloader that was based on optiboot (a bootloader that Arduino boards use).
Yes, you can flash programs from an SD card just as you would flash it via ISP or TTL.
ATmega328 is self-programmable, meaning that it can read a stream of data from an SD card (i.e. a HEX file stored on an SD card) and modify its own flash memory.
The bootloader is the part of the flash memory that is not edited and is responsible for self-programming of the microcontroller.
You can find the bootloader here:
Also, you can read more about it here:
If you were to replace your ATmega, the easiest way to flash it would be using Arduino IDE + USBasp board from ebay (costs USD5).
You can find more about bootloader flashing here:
I hope this helps and I am really glad that your build works
Please, share some photos of your build here:
See you around!