If you want to add files to the sd-card there is a lot easier ways to do it:
Select the dialog/connection window, where you connect the Axoloti. Then select the drop down menu called "board" and then select "Enter card read mode". Then the sd-card will be mounted to the computer and you can copy files to the sd-card like you normally copy files on a computer. Be aware that this function is a bit slow, it takes a while to enter card read mode and also takes time to copy the files.
If you have an USB sd-card reader, you can put the sd card into that and put it into the USB port of the computer and it will be mounted like any other harddrive. Then copy files to it, like you normally copy files on a computer. This works a lot faster than options 1. I prefer this method, cause it's faster.
Using both ways, you can copy the files to any directory on the sd-card, create new directories and so on, like you do on any harddrive or usb stick. I never used the file manager, to be honest.