I take thyroid medication with food and I feel better then when I take it on an empty stomach. Is this ok to continue to do as long as I feel good?

Empty stomach. Synthroid (thyroxine) should be taken on an empty stomach as this would increase absorption. However, I have pts that take it with food. My recommendation is to get TSH levels checked more frequently. You should avoid taking it with walnuts and high-fiber foods.
Thyroid on empty. Most synthetic thyroid medications are absorbed best on an empty stomach. Taking the drug with food could decrease the ability of the drug to be absorbed and make it less effective. Keep doing what you are doing; your physician should periodically monitor the effect of your drug, so you can know how well it is working.
Consistency is key. If you feel better taking your synthroid (thyroxine) with food, then you can continue to do so. Just be consistent and always take it with food so your blood levels of thyroid hormone doesn't fluctuate too much.