There is a philosophy in yoga that the best way to prepare for a particular pose is by doing that particular pose!
Thus, if you want to be able to sit on your heels longer, then sit on your heels more. One way to do this is to develop a new life habit of sitting on the floor!
Living on the floor has been discussed in other threads (I highly recommend you read this
thread.) Sitting on the floor may work wonders for your hips, lower back and knees. But, like with all exercise or medicine, start with small doses and work towards more time on the floor over time. Eat meals at your coffee table. Put your computer on your coffee table. Watch TV while on the floor. You'll be amazed at how effective this can be, but again don't overdo it in the beginning.
Good luck!