I'm a 100% owner of an s-corp. When I pay myself, I transfer money from my corporate account to my personal account and it's characterized in QB as "employee salary" -- okay. However, when I make estimated tax payments to the IRS and to the FTB (California), my understanding is that that is also my compensation, being withheld by the s-corp. What should I characterize those payments as? Now that I am doing my business takes using TurboTax for business, it is not catching those estimated tax payments as my "employee salary" and the numbers don't add up.
you need an education in S-corp payroll and payroll taxes. generally, an S-corp must pay its active shareholders a salary. quarterly it must file state and federal (form 941) payroll tax returns to report the salary paid, the payroll taxes withheld and the corp's share of SDI, FICA and Medicare taxes. In addition, unemployment payroll tax returns may be due for the state and at year-end for the federal (form 940). The corp makes the payroll tax deposits, not you. also, the S-corp must file form W-2 and W-3 with the Social Security Adm and state by 1/31/2022. it appears you have done nothing like this. you have a mess on your hands. find a tax pro that will help in getting things fixed as best as possible.
I did the w-2, and I did report to & pay EDD (at the end of the year) but I didn't do quarterly 940's or 941's. I did make large quarterly estimated tax payments to IRS & FTB.
Seek local help to get your payroll mess cleaned up and get an education in keeping your books. The QB program will complete the payroll nicely if you know how to do it correctly. QB will do everything you ask it to do the problem is knowing what you need to have it do.
your S-Corp needs to file payroll tax returns for the salary it paid you.
here's a link to what it looks like and what gets reported
https://www.irs.gov/pub/irs-pdf/f941.pdf
California forms are not available since they must be efiled
but here's a link to the payroll tax page
https://edd.ca.gov/Payroll_Taxes/Forms_and_Publications.htm
the S-Corp not you is required to make timely deposits for the withholding, FICA and Medicare taxes. For the state any withholding taxes and any other employee or employer taxes that need to be included on the return. failure of the S-Corp to file the returns and remit the payroll taxes could result in substantial penalties for the S-Corp and you since you are the responsible person for seeing that payroll tax returns are filed and the payroll taxes are deposited. As I said see a tax pro. if you do nothing, sooner or later your S-corp will get a letter from the IRS since they will have the W-2 (they get a copy from the SSA) but no matching payroll tax returns and there will have been no payroll tax deposits.. you may even get a notice from the state even sooner.