Almost certainly fungal infections. The infection comes from the soil, and soil that gets kicked up on the plant does the infection. Lower stems are affected first.

How do I stop this or use on the plant I think I do have Neem but not sure if it is used for that or if I need to use anything.

I have both Copper Fungicide and Daconil not sure which is better and if I should use it on the whole plant.

Saturn

Fungicides are tricky. Different fungi are treated best with different fungicides. But you might just use both copper and Daconil alternately and hope for the best. Certainly use them on the whole plant. Once established, the infection will propagate upwards. Not sure if Neem is really a very good fungicide. Note that fungicides won't cure a fungal infection, but just prevent it from spreading.

When you say ‘stems’ do you mean actual stems or leaf petioles? Can you show pix of the problem?

I prune off lower branches as the tomato plant grows. Keeps things tidy in my garden.