And the real question was estimated tax. Yes, your wife will most likely need to pay estimated tax on the net income after expenses. Due dates are
April 15 for income from Jan-March
June 15 for income from Apr-May
Sept 15 for income from June-Aug
Jan 15 for income from Sept-Dec. (they are not all 3 months each)
Payments can be made on the IRS web site, be sure to indicate that the payments are for a 2016 form 1040ES and be sure to use your wife's SSN on the payment
https://www.irs.gov/payments If you are already planning to file jointly and have your withholding set up for your normal situation, then the estimated payment should be 40% of the net income after expenses (15% self-employment plus 25% federal). You may also need to make an estimated state tax payment (3-10% depending on the state.)
For a more precise estimate you can use form 1040-ES or Quickbooks self-employment edition.
If you are already having enough tax withheld from your regular paychecks that you expect a refund larger than the estimated tax payment, then you can skip the payment and just get a smaller refund.
