You are correct that the $600 is over the entire year. You should have been issued a 1099Misc.
Your return will not be flagged for this and this situation is actually more common than you think.
You would go ahead and report the income as General Income in business section of the Self-Employed program you have. It is right after the income from a 1099Misc. Your obligation remains the same to report all of your income regardless if you got a 1099Misc or not.
You do not need to provide any evidence when you file, other than listing all your income and expenses.
The W-2 will be reported on the same return, just in the W-2 section.
You are not in any trouble for not receiving a 1099, and after you finish your return and file, you can call IRS (1-800-829-1040) or send then a letter with the detail about not getting a 1099Misc from this company. Provide detail such as name address and phone number so IRS can contact them.
