I would absolutely NOT suggest using software for filing business taxes. The laws are constantly changing, and the tax software may not have all the regulations in place for your area. If you make a mistake you will likely get audited. It is worth the money to pay someone to do it - if there is a problem, they have to answer to the government first.
Small businesses are easy targets for audits. We have owned our business for 9 years, and have learned a few lessons the hard way. I cannot recommend a qualified accountant enough.
Better everyone think your a fool, than to open your mouth and prove them right.