Technically, Yoga Nidra is supposed to be yogic sleep, and is practiced lying down. Benefits can be obtained from the deep relaxation. Meditation with specific EC intent should be done sitting up, since you are generally more alert. Yoga Nidra can be useful to access the subconscious; however, you may be too sleepy to take advantage of it and to apply the EC steps. See how it works for you. If you are able to process suppressed feelings coming up, then it is working.
Releasing the samskaras sounds good, but I don't think it happens just by going into the yoga nidra state. I would say there must be alert conscious awareness of the feeling and the EC process.