Here is a little tutorial for those who haven't succeed yet

A big thank you to Jeff and kitahei88 for their continious help.
If you plan to use the USB version of HxC, you'll need 2 boards (otherwise X68000 won't startup).
Also if you have (or plan to buy) a X68000compact or X68000pro, sorry this tutorial won't work for you (you'll have to build a different cable, which is not an easy task).
If you plan to use the SD version of HxC, it will work with two boards or a single board (emulating 2 drives).
First you need to get a floppy cable (standard one with three 34 pins ports) and have to cut the following wires (1 is the red/pin 1 wire) : 1, 3, 5, 7, 9, 11, 13, 15, 17 and 19 on the straight part of the cable.
Be sure to not cut other wires !
Here are some pictures if you are not sure (cut part 1):
http://www.retrospecies.org/upload/Cable.jpg
http://www.retrospecies.org/upload/Wires.jpg
After that open your X68000, and locate the floppy cable.
Remember where is pin 1 (red wire) then remove floppy cable from the mother board (you don't need to disconnect floppy drives).
Then connect instead your new home made cable (part 1 connected to the mother board).
Be sure to reconnect the red wire on pin 1.
Now connect to HxC (again, be sure you connect the red wire on pin 1).
If you are using SD version, adjust jumpers according to the manual (shutgart) : pin 0 for drive A (part 2 of the cable) and pin 2 for drive B (twisted part 3 of the cable), or pin 0 for drive A and pin 1 for drive B in you are using only one HxC (connected with part 2 of the cable).
Be sure that SD cards are set to "Shugart".
If you are using the USB version, follow these recommendations :
- connect both boards to the same PC (yes, it works !)
- do not use a USB hub
- do not connect on the same port
- use latest version of HxCFloppy Emulator software (v1.5.0.0)
- open two sessions of the software at the same time
- set the first one to "Generic Shugart" and DS0
- set the second one to "Generic Shugart", "Twisted cable" and DS1
- increase packet size to 2048 for both
Load your game and enjoy !
What is still not working :
A. HDM files (I don't know why but it takes 10 minutes to start).
So be sure to use XDF images.
Jeff, can you have a look at this ?
B. Softwares using auto-eject (it enters in endless loop as it cannot verify that floppy has been removed).
kitahei88 is working on this already and is thinking about two solutions :
1. Making a simple board to emulate this feature.
2. Connect the needed wires to the real floppy drive.
But in both cases, we need to find a way to automatically eject the image disk from HxC (SD or HxC software for USB version).
Jeff, do you think this can be added to HxC ? (if we provide you the required information).