I've got my knees into abit of a pickle myself after doing supta virasana, the other common one next to padmasana( for which i have'nt personally had problems)
I would suggest you
1) stop doing what you're doing,i.e trying to get into this pose if you cannot do it safely
2)Rest -take it real easy
3) if you are reallly stuck and getting no relief, consider exploring very gently this movement i'll paste a link/URL to- it's documented on u-tube. i believe this helped me in fact re-align the knee joint better and integrate them with the hips and ankles after getting into a pickle doing supta virasana. it's from 'hanna somatics' and if done gently, according to first principles, it is anatomically safe. (Just ignore the cheesy music) Some might say harmless, if done gently.
I would suggest you consult Somatics by Thomas Hanna for better and complemetary instructional audio guidance too, if you are really intereste in learning this ( as there is some learning curve involved, to do it effectively)Rotate from your HIPS , not your knees( as technie hints at you should be doin, and also IA)
When the knee moves in, to the medial line of thebody, rotate that same hip inwards.( don't drag the left foot so far outwards as the video maybe suggests but keep in line with shoulder. this is how Hanna's wife does it. and i think it's safer)
When thesame knee/ankle/leg , points outwards, observe the lift and rotation of OPPOSITE hip inwards and employ this to facilitate the movement.
You want to do it in a lazy fashion, just like a cat stretching, as Hanna suggests( why he calls his main series, designed to defeat the process of aging which he thinks is myth btw ,'the 'cat stretch'), though there is no actual stretch in fact involved.
Also you want to do it according to first principles- there are 2 main ones
1) Use the least possible effort. In addition try, as best you can, only use those muscles which are actually involved in the movment
2) Go slowly- so your brain gets time to get uncluttered neural feedback. no superfluous "noise" if that makes sense in terms of youur senssory ffeeback and neural reprogramming.
3) Focus on the internal sensation of the movement. This is acheived by 2) i.e going slowly. Put your ( maximum)awareness into the areaof the body you're working on releasing.
Another important thing-Feel the muscles contract and then slowly release in a slow controled fashion( any jerkiness should decrease as muscular control increases; you may find your strength increasing dramaticaly (as half of strength is coordination, i'm inclined to believe). The relaxation phase is important- give your attention here..This is the 'controlling moment' as they call , where new connections and pathways are instantly created, as if by magic ,in the brain( specifically, the neocortex i think, believe. we are the only animal with such a development, the new brain neuroscientists call it)At that point muscle tonus drops.( and the reflex is switched off,if i'm correct here)
With this pareticular movment ,Drag or rather slide the foot, if neccessary,at least until the muscle tonus of the legs have dropped until you can lift the leg without say incurring possible spasm the movement might elecit byt using to much effort and yourmuscles being at too high a level of tonus .
It took me six month to get some handle on how to do somatic exercises because of the learning curve involved.,hence the long description given here.
The muscle tonus./tension in your legs should reduce after doing this movement, in the way I suggest.. Relationships between hips,knees and ankles will be better integrated.Remeber – Remebr -rotate and openn from the hips, not the knees.
When I researched supta virasana-(and I read a lot fo contradictory and therfore confusing guidance I must add) I read that lateral movment in the knee joint is only possible during flexion and even then, it is only minimal , if I am not mistaken. The knee joint does not have lateral movement , not designed that way,when it is locked straight during extension( assuming that is the correct term). Yoga journal is quite good for adivce on how one can do this pose safely but if you cannot get into this pose mu suggestion would be, not to even bother. Some yogis sayit is alright for folk- I would have to disagree.
You can read more on hanna somatics here
And I would suggest you get Hanna's book Somatics and/or audio instructional guidance to guide you and complement the instructions i've given here( which are possibly not enough) and learn the movements like this one, the one I post a u-tube link to.
This is what I would explore , do( and have done), if iever, heaven forbid, got my kness in a pickle after doing a particular asana.
I remember a tai chi teacher hinting you really want to look after your knees( i.e not mess about with them , by putting unecessary strain on them) and that they don't heal so well. Their ROM is obviously lot more limited compared to say the hip socket .understanding at least how the joint works, was a great help to me.( as I say Yoga Journal has good advice on how to do supta virasana say, safely-ish, [providing you listen to your own body) Stay clear of these poses, if in any doubt.
Forgive me for the length of this post, but I felt compelled to share some things i've learnt.
And perhaps my suggestion might help.
Also, feel free to correct whatever i've said here, if there are any point about anatomy tsay hat are technically inaccurate.
Hanna somatics is basically about learning to sense and therefore control one's own body. It is a form of bio-feedback muscle-brain training, and I am still learning how to do them,'somatic excercises' ( whole body integrated movements), to produce the most effective results. I believe i'll get there eventually and believe in it's efficacy, otherwise I would'nt try and promote it here to some degree.
Of course use some common sense here, &
Listen to your body.
It's all too easy to see a yoga pretzel diagram , picture and read very detailed instructions, even after much research, and think- yeah i'll ty and replicate that.But if the boyd is'nt flexible, open, intergrated , well aligned and prepared enough for it- ti's just asking for trouble.I've done it myself with reclined supta virasana( including experimented with bolsters which is somewhat safer if you get the requisite heights just right- there's obviously an art to this)), and my knees have not liked it.
I think this goes without saying.