PC based payroll software may be a good choice for you. If you just need to handle payroll job, you can select stand-alone payroll software, such as ezPaycheck payroll software. If you need more functions, you can try QuickBooks.
Following is an article on "Accounting Suite Vs Stand Alone Payroll Software". You may like to read.
The IRS default treatment of an LLC with multiple members is a partnership, (though it can also be taxed as a C corporation if you so choose). A single member LLC is treated as a disregarded entity. This has major implications for both taxation and payroll. There's also a status known as a "qualifed joint venture", in which the couple has to fulfill certain requirements and then are each treated as sole proprietors...but I'm not going to go on about that and confuse you even more. At the state level, husband-wife businesses can be treated and taxed differently depending on if you're in a community property state or not.
Not having much info about your original filing, state, or business venture, you should really talk to a professional in your area. In some cases, it makes a lot more sense to set up the LLC with a single owner (who takes owner's draws), and the spouse as a contractor. But again, several ways to do things, case by case basis. You really want to set things up in the most beneficial way to begin with, saves a ton of headaches in the long run.
A lot of great advice in this thread. Please keep it coming!