Hi @Danni M
The payments you're taking out of the business are Drawings or Owner's Withdrawal (you should see one of these categories depending on which version of QBO you're using).
At the end of the year, the business profits are calculated & tax paid. The remainder is Owner Equity (equivalent to your take home / bottom line pay) & this is the pot from which you're taking the Drawings.
Until this is all worked out, you are effectively taking money out of the business which has not yet been taxed - so you need to keep track of it & make sure there is enough in the pot every year to pay the tax.
Hope this helps.