tbh i don’t if it will be possible to do this using x360ce as a workaround, you could ask on their forums until citra devs can take a look at this issue.
i saw that you can set the gamepad GUID on the [Mappings] section, (with x360ce closed) you could edit it either the USB or bluetooth as the PAD1 and the other PAD2 and on x360ce on the PAD2 tab, go to the tab advanced and enable ‘Combine this controller’ and combine into ‘One’, save and try it again. but as i said before x360ce may not work, so ask help on their forum for proper support.