It's been discussed numerous times in the two xDuoo X3 threads. Rockbox sees mSD1 as internal and mSD2 as external. My recommendation for file management has always been to revert to the factory firmware mode using the dual boot feature. As for accessing the files in Rockbox, go to Files, then highlight <microSD1> and press the large play-pause bottom on the lower right. You'll now see the files in mSD2.
But Rockbox merges the two databases right? You get the option to browse via the id3 tags (so Album, Artist, Genre) as well as by File (in which case you will see two options, internal and external to navigate).
I am personally not interested in the X3 currently, but might be helping someone else with the purchasing of one, I'm curious as to say why you think using stock firmware for file management is better than rockbox?
So say you have two 128gb sd cards in x3, both full of music as well as one being successful with a rockbox port. When that user browses their music via the id3 tag method does only ONE sd card show up the contents? Past experience has taught me that both internal and external mems are used in that database (ie it is possible to 'Shuffle All' tracks from both sources).