The best way for you to sit at a computer is which ever way is most comfortable for you. Most physicians would say that upright posture is better than being slouched. Also most physicians would advise you to get up, stretch, and move around for 5 minutes at least once an hour when you are at a job that requires many hours of your time at a desk or computer. Sitting cross-legged is (in general) not associated with any major health problems. With that said some people report that their legs or feet "fall asleep" often when they cross their legs. This is caused by a drop in blood flow to the lower legs because the blood vessels are getting kinked. While this probably not a cause of any long term problems, it can be uncomfortable and increase your risk of falling.
I suggest that you schedule an appointment with your primary care physician
. He or she will be able to ask you a list of questions about any symptoms you may be having and perform a thorough muscular and skeletal exam. Your doctor
may have some recommendations on how you should be sitting, or perhaps accessories to your chair that can make you more comfortable at your desk.