"I was under the assumption that I need to enter in the 1099-NEC's on the "1099-MISC/NEC" page in ProConnect and I was good to go."

Does ProConnect not have a note like Lacerte does, that says "only enter your 1099-NEC here if you have withholding from this handful of states"? That screen is strictly for state efile compliance.

Prepare your Schedule C using the Schedule C input. Report all your client's income, whether they got a 1099 for it or not. SE tax adds up quick!