Open your kua while doing horse stance. You should notice an immediate lessening of tension on your knees. Also, make sure your knees are pointing in the same direction as your toes. If you have your toes at 45 degress to your hips, make sure your knees are facing in that same direction. Toes straight ahead? Point your knees right at 'em.
Either way, open that kua if you want to last a long time in horse stance.
Relax your knees by first relaxing your toes, then your feet, then your ankles, then your calves and shins, then your knees, keep going up to relax your thighs and then your hips, then your waist and belly, up to the shoulders, the neck and then your jaw, keep going so you don't forget to relax your eyebrows. Now, start at your eyebrows again and consciously go all the way down and push all the tension you can still feel right down your body and out your toes into the floor.
Imagine a pole coming out of your sphincter that goes from the heavens through your spine, out your orifice and down to the center of the earth. This imaginary pole is both rooting you to the earth and holding you up as if it was a small stool for you to sit on.
Keep your hips tucked in, but relaxed.
Use the third eye, keep the other two closed.
Don't forget to breath. In.... Out... In... Out...
Very slowly, in through you nose, out through your mouth.
Keep your tongue on the roof of your mouth, loosely held to your palette. Don't let go to breath out, you can blow around your tounge. Don't open your mouth too far to do this, only a tiny bit, if you're breathing slowly and correctly you won't fill your cheeks up with air, it should flow smoothly out.
If you accumulate any salive in your mouth during this, swallow it naturally instead of trying to expel it.
Keep you hands folded at tantien level, right hand thumb touching across all fingertips and inside a cupped, upturned left palm, left thumb touching the accupoint at the second joint of your left index finger. (For laughs and giggles, reverse this from time to time).
Relax your shoulders, let your elbows hang, open your back, don't slouch.
Back straight, crown of the head lifted and as if suspended from above. Keep your chin tucked in.
Don't forget to breathe.
Got all that?
It has taken me sixteen years to be able to hold a horse stance for over an hour with no discomfort.
These are all the "tricks" I've had to learn to do so.
Hope this has been informative for you.