Default channel file

The channel file describes the sensors used for the acquisition: position, orientation, name, types, etc. It also contains the projectors that were computed during the pre-processing (EEG re-referencing, SSP or ICA artifact cleaning).
A channel file can be shared between different subjects or folders, but it means that all the recordings related with it must share the same SSP/ICA cleaning procedure.
To estimate the source activity, you have to compute a head model and an inverse solution for each channel file, so if you share this channel file between several subjects or conditons, you can decrease significantly the computation time and the amount of hard drive space required.

- No, use one channel file per acquisition run (MEG/EEG)
Do not share the channel files between folders. Select this option if you may have different sensor positions for one subject, or multiple acquisition runs with different SSP/ICA projectors. In MEG, this is a common setting: one recording session is split in multiple acquisition runs, and the position of the subject's head in the MEG might be different between two runs.

- Yes, use one channel file per subject (EEG)
Share the channel file between all the sub-folders of a subject. You need to define the positions of the sensors for each subject. This is a common setting for EEG: the electrodes are in the same position for all the files recorded on one subject. But never use this option if you have multiple acquisition runs and plan to correct for artifacts with SSP or ICA separately for each run.

- Yes, use only one global channel file
Share the same channel file for all the subjects and all the conditions.
This is never a recommended setting. It could be used in the case of an EEG study where you use only standard EEG positions on a standard anatomy, but only if you are not doing any advanced source reconstruction. If you share the position of the electrodes between all the subjects, it will also share the noise estimates and the source models, which are highly dependent on the quality of the recordings for each subject.