You should be fine just replacing one pickup first. In my experience a crappy pickup and a good pickup together still sounds better than two crappy matched pickups together. However since its epiphone pickups we're talking about I suggest you replace both, since that will be a huge help. That is if you really like the guitar. If the guitar is bad its not going to make a huge difference, but at the same time if you get another guitar later you can still just take those pickups out and put them in that one. So basically my answer is if you can afford it replace both, otherwise replacing the one you use more is perfectly fine.
Since you said you like the sound you're getting out of your neck pickup then I suggest just replace the bridge first, you never know, they might compliment each other really well and sound wicked in the middle position.