FreeTaxUSA actually handles Schedule C pretty well! I've been using it for my side gig for 3 years. The interface for business expenses is straightforward and they have good explanations. The best part is they don't charge extra for self-employment forms like some other providers do.

Is there a deadline for when you can still amend your return if you find the missing W-2 later? I'm in a similar situation and wondering how long I have to fix things if I discover more information after filing.

You generally have 3 years from the original filing deadline to amend a tax return. So for 2024 taxes (filed in 2025), you would have until April 15, 2028, to submit an amended return using Form 1040-X. However, it's always better to get it right the first time if possible. If you know you're missing information now, using the substitute W-2 form (Form 4852) or requesting a wage transcript from the IRS is a much better approach than filing incomplete information and amending later.

Good luck getting through to them! I tried calling the IRS last week and was on hold for 2 hours before giving up. Their phone lines are completely overwhelmed this time of year.

Thanks for the explanation! Do you know if there's any legal requirement for which method employers use? And would switching to a salaried position solve this problem, or would we still have issues if she took unpaid time off?

There's no legal requirement for which withholding calculation method employers use - it's usually determined by whatever payroll software they've implemented. Some systems allow changing the method, but many smaller employers are locked into whatever their provider offers. Switching to a salaried position would generally solve this problem since salary typically means consistent paychecks regardless of hours worked (within reason). Even with unpaid time off, most salary calculations are more consistent with withholding. However, part-time salaried positions are relatively uncommon in pharmacy settings. Another option is to ask if they can set up a "minimum withholding" arrangement where taxes never exceed a certain percentage of gross pay.

This is smart advice! My paycheck once went to zero and I assumed it was taxes, but it turned out they were taking uniform fees, health insurance for the whole month, and a retirement loan repayment all from one small check. Worth investigating all deductions!

What counts as "proper documentation" for R&D? I keep all my receipts and invoices, but do I need something beyond that to show the experimental process?

Receipts and invoices are a good start, but they're not enough for R&D credits. The IRS wants to see evidence of your experimental process - essentially documentation that shows you were solving technical problems through trial and error. Ideally, you should keep project plans that outline the technical uncertainty you were trying to resolve, lab notes or development logs showing different approaches you tried, test results showing what worked and what didn't, and meeting notes discussing technical challenges. The key is demonstrating you didn't know the outcome in advance and used scientific principles to find a solution. These records should be created during the work, not after the fact when preparing your taxes.

The Employee Retention Credit (ERC) was generally available for wages paid before October 1, 2021. However, there was an exception for recovery startup businesses that could claim it through December 31, 2021. For 2023 tax returns, you can't claim new ERCs, but if you had previously unclaimed credits from eligible quarters in 2020-2021, you could still claim them by filing amended returns (Form 941-X) for those specific quarters. This wouldn't go on your current Form 3800 though - it's a separate process through payroll tax filings.

How do you qualify for their help? Do you need to show proof of hardship or something? My CP2000 is for $4k and there's no way I can pay that right now.

You need to demonstrate that the tax issue is causing you significant financial difficulty or that the normal IRS processes aren't working correctly in your case. Examples would be if paying the amount would prevent you from affording necessary living expenses or if you've made multiple attempts to resolve the issue through normal channels without success. You can call them directly or fill out Form 911 (Request for Taxpayer Advocate Service Assistance). You'll need to explain your hardship situation clearly. For your $4k situation, if paying that would prevent you from paying rent, utilities, or medical expenses, that could qualify. They can sometimes help set up manageable payment plans or put a temporary hold on collection activities.

I used the payment plan last year. It was actually pretty straightforward. You can set it up online for smaller amounts or by phone/mail for larger ones. Interest still accrues but the penalties are much less. I did $100/month and it was manageable.