There is no such thing as a 1099 employee. If you are paying an other company for work they do for you, that is a 1099 vendor. See the attachment about the difference, it can get very expensive if the IRS or the state decides what you think is a 1099 vendor is really an employee.
There is no QBO Pro, Pro is a desktop version, there is QBO simple start, QBO essentials, and QBO plus - I think you mean plus since that is the only version that tracks 1099 vendors
It is six of one half dozen of the other as to whether you spend the time entering things into QBO or not. If you have assets, or liabilities QBSE does not handle those. QBSE does not do sales tax either