My boyfriend and I moved in together last week and things have been going very well for the most part except when it comes to the kitchen. He was raised kosher style while I grew up keeping kosher. Before we moved in together, in the beginning of our relationship, he said it was his place, as the less observant person, to adapt to my level of observance (a fact of which I am very appreciative and was an important thing to discuss as things were starting out). Now that it's actually taking place, he is fine with the two sets of dishes and silverware but is uncomfortable with the parve items (mainly knives and cutting boards). We have already labeled the cooking utensils with different colors of electric tape and have organized the cabinets and drawers in a way that makes sense in the placement of the dairy and meat dishes. Do you have any other suggestions about "teaching" someone about keeping kosher?
Your question reminds me of another question I answered  almost exactly a year ago from someone else in a relationship with a partner accustomed to a different level of kashrut observance. You're not alone in wondering how to navigate this often difficult situation. It sounds like your boyfriend is both respectful and accommodating, so you're off to a great start and should be able to find solutions that work for both of you.
What is it about the pareve items that's causing him discomfort? Is it not being sure when and how he can use them? Is it confusion over where to store them or what sponge to use to wash them? Is it being utterly baffled that there is yet a third variety of dishes he didn't know about? Whichever it is, I must say, I sympathize. Though I grew up in a home with two sets of dishes plus a variety of pareve knives and other utensils, what, exactly, to do with the pareve items never became clear. In my own home now, as an adult, items are either dairy or meat. (I also happen to be comfortable with a more liberal definition of when "dairy equipment" can be spun as pareve, but that's another and far more complicated story).
It sounds like you've done a great job labeling everything. Make sure that pareve items have a clear label as well. Perhaps on the door to the drawer with the pareve knives and cutting boards, you could have a checklist of what foods are pareve (essentially fruit, vegetables, eggs, fish) and some quick guidelines about where to put the knives after they've been used, or something like that. You could also consider, for your boyfriend's sake, having some quality meat and dairy knives and cutting boards so he doesn't have something else to worry about. You can use the pareve things when you cook, but you could take that burden off of him.
If your hope is for your boyfriend to internalize keeping kosher on some more fundamental level, that may just not be possible until he's had a lot more practice. The practice of kashrut is, when you really think about it, not that intuitive unless you grew up with it. Even then, "keeping kosher" means so many different things to different families that there's no guarantee that what it means to you matches up with anyone else. As I often say, everyone makes their own rules, and that may be the most true when it comes to kashrut. Also as I often say, I recommend myjewishlearning.com as a great resource for learning more about basically anything related to Judaism. There are an unlimited number of books about keeping kosher available, but it's probably best to peruse them first to be sure that they match up at least reasonably well to the kind of kashrut you want in your house. Kosher cookbooks also often have great introductions outlining some of the basics, and, in my humble opinion, cookbooks are more fun to own than books of laws. Be as kind and respectful of your boyfriend as he is being of you, and I'm sure your kitchen will be a wonderful place.