Good question. Your MC will be the best to answer this. Because it won’t count toward your qualification income I’d be inclined to say you don’t need to upload the paystubs to your file. I would just make sure you keep all the paystubs in your own file so if you are ever asked why you have large deposits you can easily produce the evidence.
You might have to, if the second income funds will count towards your MRF and buydown to show source of funds. It wont count towards qualification since the income isn’t 2yrs established, so it wouldn’t affect whether you are priority or non priority mbr, or your PITI amount