In general, I would not recommend putting anything in the bottom of pots, especially anything that can clog up/inhibit water to drain from the pot; I suspect magazines would do this. Water should freely drain from the container or root rot will result.

If I already have the magazines in the bottom of pot with tomatoes planted is there a way to help my problem? Can I drill Holes in the side at the bottom of the pot to let water out and air the roots?

If the magazines are hidering the drainage of the original drainage holes, you can drill through the holes and the magazines to open them up. But, as you inquired, you can also drill holes just above the layer of magazines on the sides to allow for additional drainage.