Hi Jack,
If siddhasana causes knee pain you can use a prosthetic like a rolled up sock instead of your heel. That way you can use pretty much any sitting position and still gain the same benefit as from regular siddhasana. This even works in a chair or on a meditation stool.
If you want to use siddhasana sitting cross-legged on the floor and use your heel then you may find using a cushion or two under your spine will help. By raising the spine upwards it changes the angle of the knees and so causes less pain. You need to position the cushions in a way that there is a space under your perineum for your heel to rest without there being too much pressure on the perineum. A zafu is by far the best for this as they give more support than a cushion or two which tend to be soft.
If you want to do asanas that will help you to be able to get into siddhasana without knee pain, then I would recommend the following:
Sitting toe touch,
Butterfly (badhakonasana),
Sitting, legs apart and head to the floor
Sitting, legs apart, head to one knee and then the other
camel (ustrasana)
Virasana (hero)
reclining virasana
bridge (setu bandhasana)
anjaneyasana (3 versions, arms straight up, arms back, twist to each side)
Apart from the first one these are all hip openers. With open and flexible hips it is much easier to get the knees down whilst sitting and to be able to bring the heel under the perineum at the same time. Then there is much less chance of getting pain in the knees. All of these asanas are ones that we have done on the last two U.K. retreats so you will be familiar with them.
Christi