I have a single-member LLC (with S-Corp designation) in NC that focuses on IT consulting. I track all my business expenses via simple google spreadsheet and hand over the spreadsheet plus the W2 income statements to my CPA at the end of the year. I pay the CPA about $900/yr for the Schedule K1 and pay about $50 to freetaxusa for personal taxes - including both federal and state taxes. This seems to work well for me.

In previous years, I did payroll manually (by hand), but moving forward, I have decided to use Square to pay my W2 since they properly track and file all state/fed tax forms. Less headache and stress at the end of each quarter. Worth the $40/mo in my opinion.

The only gotcha to my approach (CPA + freetaxusa) is you need to be your own tax "champion". That is, you must research and understand what tax deductible options are available for your business. For example, since I have an S-Corp, I can deduct health insurance, SEP-IRA (25% of W2 income), mileage, and any business-related expenses (hardware/software/office/etc). There are some other interesting deductions that push the limit of what the IRS will consider (eg: use your house as a business meeting place for less than 14 days/yr, use a second home to keep/store data off-site, etc), but I tend to shy away from those since they don't provide any real savings but raise flags during tax reviews.

Finally, get smart on the W2-vs-distribution method of pass-thru income. W2 income requires you to pay fed, state, and self-employment taxes, while the distribution method does not pay self-employment taxes. In general, you can pay yourself 50% W2 income + 50% distribution income and not raise an eyebrow at the IRS.