Would it be better to have my new employer pay me a sign on bonus or have them pay the mortgage company on down pay on new home purchase? Florida, do not own a home since 10/2004. Married w/ no dependent children. Salary is 100K ann.

Doesn't matter, at least from a tax point of view. In either case you'll pay taxes on the bonus. If your employer is going to "true-up" the bonus to cover the additional taxes you owe, then even if they pay the mortgage company directly they will still need to issue you a check for the true-up amount.