For those who are/have been self employed, what's your advice on paying yourself as a 1099 contractor/sole proprietor(payroll tools, book keeping, deductions, accountants, maximizing take home pay)?

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S-Corp all the way

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With a LLC you can do a SEP-IRA and also put away 25% of your salary. LLC is a bit simpler for paperwork I think, but depending on your circumstances there may be reasons to use an S-Corp. my accountant steered me to a LLC.

When I was doing independent work, I made a LLC and used a local accountant to advise me, and then just followed his instructions.

I didn’t need anything like Quickbooks, the accountant would just tell me what to pay to each taxing body at what times (generally once/quarter). He also advised me on how much to pay myself in salary vs. owner distributions, which often can be geared to how much you want to put in tax deferred retirement accounts (e.g. SEP-IRA).

If you have employees, or if your business is more complex than just billing clients by the hour or project, then you may need something like quickbooks to deal with payroll and other operations. In my case it was pretty simple, and all the transactions the accountant needed were primarily in the business checking account.

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A local, professional business accountant was worth his/her weight in gold! Saved me so much money.

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You should spend some time in your own books for a while before having someone else do it. You'll learn alot and can give your future accountant/controller better guidance on what you want or dont want.

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