What I do is edit the channel file naming the reference "EEG-ref" and the others EEG
Why do you need to rename channels?
Are you changing the NAME or the TYPE of the channels?
The problem is with the external montage (body) for which I have 2 different pairs of electrodes that each need to be re-referenced to the passive ones. For example, EXG-3 reference to EXG4 with label EMG. Unfortunately there s not enough naming option possible with references for me to do so and pair them (as the only other option is MEG and I cant compute my analysis after). Can I just create new specific labels ?
I don't really get what the problem is.
I guess what you call a "label" here is the "type" of the channels?
Why do you need to change the types of the channels? Leave all the EEG (including the references) with the type "EEG" and all the EMG (all the pairs) with the type "EMG".
How do I create a bipolar montage on brainstorm from a monopolar one ? Just with the tutorial you suggested ?
What you want is to create a display where you can see both the EEG (common reference or "monopolar") and the EMG (pairs of bipolar channels)?
Start by creating a re-referencing montage to reference correctly the EEG to its reference (https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor#Re-referencing_montage) then add some lines at the end for your bipolar channels. For example:
EMG1 : EXG1, -EXG2
EMG2 : EXG3, -EXG4