Your headline about Dealing with Two Businesses mislead me. If your LLC/Sch C is getting a 1099-MISC from your mom's S-Corp, then yes your expenses to earn that income are deductions on your Sch C. Was that your question? If your question is how to track those expenses, then the answer is in the usual way you track your expenses, with a separate bank account, credit card, mileage log, etc. Just continue using your same mileage log as you use for all your Sch C mileage, noting the client, reason, date, miles, etc. Obviously, you cannot magically create business mileage out of personal mileage.
Also, be certain that you actually are an IC now that your duties have changed for your mom's S-corp. It sounds like she now has a lot of control over your activities, such as requiring you to meet her clients at her location, preparing tickets in a certain way, operating under her direction, etc. Do confirm for yourself whether you are an employee or an IC or maybe an IC for tax preparation but an employee for the S-corp's administrative duties.
Also, be certain that you actually are an IC now that your duties have changed for your mom's S-corp. It sounds like she now has a lot of control over your activities, such as requiring you to meet her clients at her location, preparing tickets in a certain way, operating under her direction, etc. Do confirm for yourself whether you are an employee or an IC or maybe an IC for tax preparation but an employee for the S-corp's administrative duties.
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