If my husband owe a large amount of tax due to being a contractor and not paying quarterly taxes is it to my advantage to file separate taxes?

Probably yes. But note that probably his income and tax liability is community property. Still it is probably beneficial. Plus, if it turns out that you could save money by filing a joint return, you can always switch up until April 15, 2017, for 2013 income tax returns, i.e., 3 years after the due date. So file separate now, and switch later if it will save money and his separate taxes have been paid.