If you are referring to /boot/efi/EFI then I think it’s likely you have a fundamental misunderstanding;
/boot/efi is not a directory structure, it’s a mountpoint 
– essentially a symbolic link which links to the EFI System Partition (ESP) – hereunder referred to as $ESP.
When you ask for a directory of /boot/efi the mountpoint is first followed to the $ESP and the contents are displayed – the single /EFI directory;
EFI
If you ask for a directory of /boot/efi/EFI the mountpoint is followed and the content of the $ESP/EFI directory is shown:
BOOT
Manjaro
Microsoft
And if you ask for a directory of /boot/efi/EFI/BOOT the mountpoint is followed and the content of $ESP/EFI/BOOT is shown:
bootx64.efi
Using the mountpoint in the path is the easiest way to access directories on the $ESP via terminal, for example when wishing to perform basic file operations such as cp or mv, or simply asking for a directory listing:
sudo ls /boot/efi/EFI/BOOT
So, that briefly explains;
Regards.
OS Separation is especially important while installing each OS, as it helps avoid clumsy situations such as what you have now experienced.
The trick is to first disconnect the other SSD;
I’d suggest installing Windows first (with the intended Manjaro SSD disconnected). In this way Windows will install it’s own $ESP to the Windows SSD, and it will be completely self-contained.
Next, disconnect the Windows SSD and install Manjaro to the second SSD. Once installation is complete (and Manjaro is functioning as expected) you can reconnect the Windows SSD.
Important:- Boot to your computer BIOS and make sure that the UEFI OS on the Manjaro SSD is selected first in boot priority. Once that’s done, reboot and os-prober should detect the Windows UEFI boot files on the Windows SSD, and offer it as a boot option.
Easy, right? 
Someone should make a tutorial – wait, someone did 
:
I hope this is helpful.
Regards.