Hello claudio,
I was very surprised at the design. These two functions are very important features of I. MX processors.
Their purpose is to provide convenient debugging and mass production for customers. In fact, before making PCB boards, you should send us your schematic and let's check the design for you.
now for your questions, I can only give you some advice, see below, please!
--how can i start u–boot?
(1) UART port doesn't support to download u-boot to Flash on board. so don't consider UART, please!
(2) JTAG interface
In theory, u-boot can be downloaded into DDR3 memory(not internal ram) via JTAG interface, after u-boot run in memory, on u-boot command line, you can use related commands, like mmc write, etc to write u-boot in memory to eMMC or SD card. This means u-boot will be written to eMMC(or other falsh) by itself.
---would you reccomend to burn the efuses?
You didn't design Boot Configuration Select circuit, so I also don't know which device will be used for booting system. If there is no way to select a boot device, you will have to burn eFUSE to select a fixed device for booting. But this requires that u-boot should be run in memory at first, then burn eFUSE on u-boot command line by related commands.
So in brief, you should try your best to run u-boot in memory at first.
Hope above information is helpful for you.
Have a nice day!
BR,
Weidong