Matching Journal Entries With Transactions

If the transactions are in the account, then there is no reason to make a journal entry.  Journal entries should be the exception when using QB, they often do not work as you think they should, and  when you use inventory type items they never work for inventory. It is much better to use the forms on the home page the way QB is designed to be used.    Journal entries also bypass accrual/cash reporting, and will not show on many reports.

If you do use a journal entry, though there is little to no reason to, no you do not use a negative number, it is either a debit or a credit entry

I have to create journal entries because we need a more detailed look at every part of our payroll. Whereas the transaction in Quickbooks is just one big overall number. Would it work to exclude the transaction and then make the journal entry? I am afraid that because the journal entry is adding the debits and credits and doubling the amount that it will process more money than actually what it was.