Yes, these forms must be handled separately within QuickBooks Online (QBO) because they report different types of payments. Let me add further on this.
First, if you paid your vendor at least $600 for rent, awards and prizes, attorney payments, and other income payments, you will 1099-MISC form for the vendor. However, if you pay an independent contractor over $600, you should issue a 1099-NEC to the contractor and tax authorities. For more details about the difference between 1099-MISC and 1099-NEC, kindly check out this article: 1099-MISC vs. 1099-NEC: Differences, deadlines.
Next, please ensure that the expense accounts are mapped correctly for each form to prevent any mixing of payments when you prepare your 1099s. You can refer to this IRS guide to help you in this task: Instructions for Forms 1099-MISC and 1099-NEC (Rev. January 2024).