There is currently no simple way to do this in NGLess (although another person asked me about it this week, so it may not be that particular of a use case).
The only way is to merge them at the very beginning, so that you have a sample which includes all of the FQ files together. I guess the issue is that doing it naively would result in duplicated computation because you would be processing the same FQ file as part of the combined sample and as part of the individual one, which is very sub-optimal.
Another way is to merge the SAM files manually outside of NGLess and then load the combined samfile in ngless.
Best