If they end up similar weights (ie, one 50g rat or two 25g mice), no, it shouldn't make a difference. It's easier for you to feed him one item, but it shouldn't make any difference to him.
If you have smaller ones you want to finish up and use, that's perfectly fine. I've done that before when I had rat pups I wanted to finish up. Lots of people have bigger ones that only eat mice and they get multiples all the time.
If you aren't sure how many to do since eyeballing for width is different with multiple items, weigh the food. Basic guideline is 10% to 15% of bodyweight. You can vary outside of that, but that's a safe, solid range. So if he weighs 180g you're looking at total food weight of 18g to 24g. Two 12g hoppers at once would work fine for him.