If it was me, I'd still do online check-in. As long as you don't indicate any room location requests during online check-in, you won't mess up the request you've already made. By doing online check-in, you can indicate what time you plan to arrive and there's a higher possibility that your rooms will be ready when when you get there. Also, you'll be able to put your credit card information in during the process. If you enter your credit card information ahead of time, there's a good chance you'll be able to go directly to your room when you arrive. If you get direct-to-room check-in, you'll get a text with your room number about an hour before you arrive. You'll be able to check with your brother to see if he got his room assignment and you'll know if you got connecting rooms. If you don't get assigned connecting rooms, you can go to the online check-in line at the front desk and see if they can change your room assignments so that you have connecting rooms. And if they don't have any available, ask if they would have something the next day. It seems like most people who request but don't get assigned to connecting rooms at check-in can usually move to connecting rooms by the next day.
Plus, as ChloeChipper mentioned, if you do online check-in and still need to go to the front desk, at least you have the option of going to the online check-in station if that line is shorter. You can also go to the regular check-in stations if that line is shorter.
Side notes:
1. When you call "Pop Century" or any resort, you're calling a call center that may not even be in Orlando (even when you dial the front desk from your room). You're not actually talking to someone at the resort. The phone CMs are notorious for giving incorrect and incomplete information. You will get better advice here from people who have actual experience.
2. I'm not sure I'm clear on your room/credit card situation so I'm just going to throw this out there as general information. If your brother's credit card was/is attached to both rooms and you make a change to have your credit card attached to your room, I highly suggest that both you and your brother make a few purchases using your MBs on your arrival day and then stop by the front desk that night or the next morning to get a print out of charges for each of your rooms to make sure everything is assigned correctly. They will be able to fix it if it isn't, but if you do that little test right away, you won't have a week's worth of charges to sort out when you get your final room charge statement.