The popular phrase is that Quicken is used to document what actually happens in/across accounts. I wish this extended to it's functionality.
For example, I have a paycheck in my Bills, Incomes, and Reminders tab that has the details for my bi-weekly paycheck, including the amounts of my paycheck that are deposited into various checking and savings accounts.
In Quicken, this is treated as a deposited into the primary account with transfers to the other accounts. In reality, the amounts are actually direct deposits from my employer into the various accounts.
This nuance messes up the ability to include paychecks in the Budgeting tool because to budget for the paycheck you can only include the net amount, which is only the amount deposited into the primary account. To budget for the amounts deposited into the other accounts, you have to include transfers to those accounts, which in turn brings in ALL TRANSFERS to those accounts, not just the paycheck amounts.