I'd definitely suggesting pumping both sides at the same time; pumps aren't as efficient at extracting milk as your baby is. Also, that may just be the natural progression of your milk coming in, completely. If your baby is only a couple weeks old, it's entirely possible your milk is still adjusting to your baby's suckle and her food needs. I was surprised, with #3 (after 45+ months of nursing) to find how long it took my milk to adjust to her needs, and how tender I was even until like 6 weeks postpartum. My breasts were achy, so it may not necessarily be due 100% to the switch to the pump. When my milk first came in with my first, my breasts were literally purple, hot to the touch, and LOOKED like someone had dumped marbles into my breasts! I couldn't handle touching them myself, so I had my husband work to extract a little milk before I pumped and before I fed. It was awkward, not at all sexual, but it helped a TON! It took a lot of the pressure and pain off the top, and I could let down for the pump and for my baby. Before that, it was just like it was all blocked up in there. Good luck; wishing your baby a speedy recovery!
Updated
I'd definitely suggesting pumping both sides at the same time; pumps aren't as efficient at extracting milk as your baby is. Also, that may just be the natural progression of your milk coming in, completely. If your baby is only a couple weeks old, it's entirely possible your milk is still adjusting to your baby's suckle and her food needs. I was surprised, with #3 (after 45+ months of nursing) to find how long it took my milk to adjust to her needs, and how tender I was even until like 6 weeks postpartum. My breasts were achy, so it may not necessarily be due 100% to the switch to the pump. When my milk first came in with my first, my breasts were literally purple, hot to the touch, and LOOKED like someone had dumped marbles into my breasts! I couldn't handle touching them myself, so I had my husband work to extract a little milk before I pumped and before I fed. It was awkward, not at all sexual, but it helped a TON! It took a lot of the pressure and pain off the top, and I could let down for the pump and for my baby. Before that, it was just like it was all blocked up in there. Good luck; wishing your baby a speedy recovery!