For (1): I’d suggest that you should NOT rely on LED’s to judge whether it is “finished”. An LED can stop blinking while a data transfer is incomplete, because the CPU is busy doing something else. The only safe way to determine if a device is safe to disconnect, is to ask the thing that is doing the writing.
When you use the “dd” command, it will not return until the write is completely synchronized;
# dd if=gpt.img of=/dev/mmcblk0 bs=1M
<output of dd command... blah blah blah>
# <-- when you see that, it is synchronized and safe to remove
Similarly, when you unmount partitions, the umount command will not return until the filesystem is synchronized;
# umount /dev/mmcblk0p20
<pauses for as long as it takes to sync the FS>
# <-- it is now synchronized and safe to remove, PROVIDING that ALL filesystems are unmounted.
For (2), I don’t know if you realize this, but the connectors on either end of the eMMC module and adapter board are actually different sized. You CAN’T plug it in backwards.