Hi Sheryll,
You will still get a benefit from lying down and meditating. There are perhaps two considerations within this. It is really valuable to let go, and it is also valuable to work with your focus within a situation where you are distracted by discomfort. Your focus can allow you to stay longer in a position. The moving between you holding the focus, and thinking about the discomfort, is valuable self awareness to work with. That switch, can be a reaction of sorts with an edge, or sort of an unware state of thinking. In a non reactive state, always returning to the focus, when you find yourself thinking that you are uncomfortable, can be transformative.
I have always had times where I may have gotten too wound up in self discipline too, and a good non physically challenging let go can also be transformative.
From a larger physical viewpoint, your meditation and active exerise, can move you towards a better state of physical health, and less discomfort regarding sitting or standing exercises.
If you choose to lie down, which is certainly fine, and you are in the good , better , best mode of operation, see yourself as progressing, through the lying down, into a sitting position, and so on, regarding better and better sitting positions. No hurry, no pressure to do that.
Let go, enjoy letting go, and also challenge yourself to sit, and try to move that along too. There isn't a right or wrong here, only more good possibility within the practice.
love,
gallen