Cukes don't like to be disturbed, so it is best to start them in pots made from newspaper wrapped around vegetable cans. Make them about 4" deep. You only want to start cukes, squash etc about 2-3 weeks before you are going to put them out, so you might concider restarting the cukes.
After you transplant the tomatoes, run a fan close to them several times a day or gently pat the tops back and forth as if the wind were blowing back and forth. That will help them to develop thicker stalks. If they are too leggy, then of course this will only help so much. You didn't say how old the tomatoes were and if they had been pricked out and potted up once or not. You can bury the tomatoes as deep as there is that fuzzy stuff along the stem, that is the area that can form new roots, don't go any deeper.