Definitely get two windows (or tabs, depending on what browser you use) up. Get each window open to the right page, enter each traveler into their own window, get each window ready to go so you just are clicking on one button each.
When the time clicks over, click on one window, see that it went, switch to the other window, click.
easy peasy.
However, you're likely to be separated by a few numbers.
If she's too young to stand by herself for a few minutes, even with you right nearby, then just have the two of you stand at the "later" boarding number. So if one of you is 25 and the other 28, just go to 28. It's really the best way.
If she's old enough to stand "alone" (again, just a few feet away from you!) but not necessarily old enough to choose the seats AND she gets an earlier-boarding number than you, you guys can take the correct positions in line, then she can hang back once she gets into the jetway, and you can board together. And of course if you're the earlier number, you just wait too.
But I will tell you, people tend to be nice when you give them the chance to be. DS and I were separated by a few numbers when he was around 3 years old, and since there's chatting going on as people sort out who has what number and who stands behind who, people quickly figured out that one of us could have been a few numbers earlier. And everyone in between our two numbers said "oh please, go up to the earlier number, it's no big deal, please". So we did.
On our trip last month, DH was booked separately from me and DS. Our numbers were such that we were on opposite sides...DH was at something like 29, and DS and I were at 33 and 34. At the line-up poles, that meant he was second to last on his side, and we were up right near the front on our side. Although our placement in line didn't allow anyone to be kind while waiting (not close enough for conversation), as soon as we entered the jetway and DS called out to DH, people became aware. Not sure why hubby didn't stop and wait for us, but we did have ONE person tell us to just go up to him. She insisted I get in front of her, so we did, but the other people didn't hear the conversation and I wasn't going to just cut in front, LOL.
Anyway, if people see you being polite and going back to the later-boarding number position, they might very well be polite right back, and let you go to the earlier-boarding position.