The QuickBooks Self-Employed (QBSE) is used for an independent contractor (self-employed) to help track their business-related transactions.
If you're starting a new QuickBooks Self-Employed and you have old W-2 income (your old job) then only the new work you do in your new company would go into QuickBooks.
In this case, I suggest consulting an accountant to help and guide how to record this. Your accountant can provide more expert advice in dealing with this concern.
I've also added these articles to know more about the different categories and how to file taxes in QuickBooks Self-Employed: