I would not use any cover crop when growing in pots, only outdoors and only if growing directly in the ground in well prepared and nutient rich soil.
In pots, cover crops tend to compete for root space with the cannabis plant and will strip nutrients from the soil that should be going to the cannabis plant. The tiny bit of nitrogen they "fix" into the soil is far less than what they rob from the soil.
I would suggest cutting them down and removing them, any "mulch" left lying on the soil surface in indoor cultivation is a potential breeding habitat for molds, fungi and insect pests as well.
Outdoors chopped alfalfa makes a fantastic mulch, but I would not plant any cover crops in any container grown plants.
While it may seem like a great idea and very natural and holistic, in reality, indoors it is more likely to cause issues rather than provide any real benefits to your cannabis plants.
If you are super keen on continuing with the cover crop, wait until it is 4-5 inches tall, cut them off at ground level then cut it into small pieces and then lay the pieces directly on the soil surface. There is no need to dig them in.