Should I take my allergy medicine on an empty stomach, or right after a meal?

It depends on if. How quickly you would like it to work. Most oral medications, if taken after a high fat meal will have a slower onset of action.
Shouldn't matter. For most allergy medicines, it shouldn't make much difference whether you take them with food or on an empty stomach. Be sure to read any instructions that come from the pharmacy with prescription medications, or in the box if you have bought an over-the-counter medication. You will probably be ok doing whatever makes you comfortable.