Currently the specification only has details on how to name a single marker file associated with KIT MEG systems (see here).
MNE-python however is able to handle multiple .mrk files and averages them if more than one is provided.
I wrote a PR to export the .mrk files with MNE-BIDS (mne-tools/mne-bids#114) but since we have no specification on what to call the files if multiple are used this PR cannot continue until this issue has been resolved.

While the majority of the time it seems only one .mrk file is ever used with any given .con file, sometimes the researchers will do a -pre and -post recording .mrk file. To this end I propose possibly having a -pre and -post tag after the _markers tag in the file name.
Eg.

sub-control01_ses-001_task-rest_run-01_markers[-pre|-post].<mrk,sqd>

Not sure if this is the best way to do it, so I am very open to better suggestions.
@teonbrooks