Start by only planting varieties that are known to be resistant to the wilts.

Are you sure that's the problem? Do a GardenWeb search on Late Blight, a scourge that devastated many tomato plants in the northeast last spring and summer.

And FWIW, you should not EVER use garden soil in containers. It's way too heavy, packs down, and suffocates the plants. When you mentioned "soil", I thought maybe you'd been trying to grow them this way. Check out the GardenWeb Container forum for great information about growing things in containers.

should I account for a crop rotation?

Sure if you have the room. Most who used raised beds don't so can't rotate. I don't rotate in my raised beds and never have.

But then I don't have a problem with the wilts. IF Fusarium or Verticillium wilt is an accurate diagnosis, and that's a big IF IMO, then using only the resistant varieties may be your only option. Or consider one of the systemic fungicides. Simple annual rotation won't provide any effective control for the wilts.

Amending the soil beds with a 1:3 mixture of high quality compost has proven to be beneficial as the compost contains bacteria that can help control the soil-borne causal fungi. Another good mix is the 5:1:1 recipe discussed on the Container Gardening and Sq. Foot gardening forums. It contains no soil - no dirt - so fungus problems are minimal.

Hope this helps.

Dave

Here is a link that might be useful: Univ. Conn. IPM : Tomato Wilts

Couple of years ago I planted tomatoes under a Black Walnut tree, they wilted and died.
I planted a second set, they also wilted and died.
I foind out later what the cause was, not fungi but a substance existed in all parts of BW that act as herbcide on certain plants.
I have heard opinions that regular Persian/English walnut also produces similar substance (Juglone) but to a lesser degree.