So I see part of the confusion. Start with a copy of form 1040 (print a blank one if you like). The front page lines 7-22 is all your income (all your joint income if you are married filing jointly.) Lines 23-37 and all the back page is all your personal deductions (standard deduction or itemized deductions, personal exemptions, tax credit for child car or electric cars or solar panels, whatever.)
If you are self-employed, all your net business income is reported on one line, line 12. The income comes from your schedule C. If you have 3 separate businesses you might have 3 schedule Cs that are combined on line 12 to give one income figure that goes into your personal (or joint) income.
For things like standard deduction, it doesn't matter where the income comes from; it could be wages (line 7), a self-employed business (line 12), selling investments (line 13), pensions and IRAs (line 15-16) or anything else.
Now print a blank copy of schedule C. Schedule C is used to calculate your net profit or loss from self-employment. (A person who has several jobs might have separate Schedule Cs, if they want to or are required to keep the profit and loss from each business separate.) Schedule C calculates your net profit or loss by taking all your gross income and subtracting the expenses you incurred in earning that income. A mechanic might deduct expenses for purchase of tools and supplies. A home health aide might deduct expenses to buy scrubs and other supplies, as well as deducting expenses for CME, licenses and certifications. If you drive a car you can usually deduct car expenses (subject to certain rules). If you have a home office, you can often deduct a percentage of your homeowner expenses equal to the percentage of your home used for business. But there are lots of rules and qualifications that need to be met, and certain potential down sides as well.
On schedule C, you deduct your expenses from your income to calculate the net profit from business. (Your spouse as a W-2 employee, can deduct unreimbursed business expenses, but only as a personal deduction on the back page, as part of itemizing deductions instead of using the standard deduction. That is much less favorable since there are several cutoffs that reduce the impact of the deduction.)
After you have your net profit or loss from all your schedule C businesses, you add up the total net profit and use schedule SE to calculate your self-employment tax (SE version of social security and medicare) and that goes on the back page of form 1040.
Any business expenses you deduct on schedule C can't be deducted again on form 1040 or schedule A.
Here are some links to look at
https://www.irs.gov/businesses/small-businesses-self-employed
https://www.irs.gov/businesses/small-businesses-self-employed/home-office-deduction
https://www.irs.gov/uac/about-publication-463
*Answers are correct to the best of my ability at the time of posting but do not constitute legal or tax advice.*
