My wife had a business last year. Should we still file our taxes jointly?

I’ve done some quick google searches on this, but figured I might as well tap the considerable resources of Fluther as well.

My wife and I have filed jointly since we’ve been married. Last year, she ran a small business that lost money. We own a house we live in, and own a property on which we collect rental income. I’m the one that does the taxes, and I find it to be a PITA since the tax software I’ve used doesn’t handle rental income/loss very clearly and intuitively. I’m thinking figuring taxes on her small business will be an even bigger PITA.

I know I could use the software to file both ways and see which reduces our tax liability the most, but if I can avoid several hours of additional work with good advice, that would be better.

Also, does having a small business complicate things to the point that I don’t want to mess with it as an “amateur” tax preparer? I’ve got a good head for numbers, but don’t want to make a significant error if it is easy to do so. FYI, I’ve used TaxAct online the last couple years, and was thinking of trying TurboTax instead. TaxAct seems better for simpler taxes. If someone has a good software recommendation, I’d welcome the suggestion.