Depends on the year as stated before.
If it is a fox body then the shorty header setups are exactly the same for auto and 5-speed. Longtubes are a different story. MAC, Kooks and a few other select companies are the only ones that make longtubes for an automatic. With longtubes, you will have to get a matching H-pipe (BBK--->>BBK) to get everything to bolt up unless you have a custom H or X made for your headers.