calibre and likebook mars transfer

I just saw a similar question on a kindle but didn't want to Hijack his thread.

I'm trying to eliminate calibre companion since it's pretty much abandoned.

If I pull the SD card and use a seperate card reader, i can transfer the books into series folders. Much easier to organize and find stuff.

There probably isn't a way to do that when directly connected is there? It just sends the files into 1 folder instead of breaking them up.

Thanks.