The first thing I would say (speaking as a designer!) is that you should not be timid about expressing your reaction to a design. You need a design that communicates clearly and accurately (or a user interface that works intuitively and effectively). This has everything to do with effective communication and the needs of the user, very little to do with the whims of the artist. Art and design are closely related, but they are not the same thing. I tell every new client up front, "When you give me feedback, don't try to be careful of my artistic sensibilities, because I don't have any. My job is to get your message to your public in the most effective way." The client is the client; that includes, if you work in-house, the boss.
You can say you love the idea (assuming that it isn't awful), but that from a usability standpoint, you'd like some tweaks. Be friendly and above all, be honest. Say what your concerns are with the reasons why, and your designer will understand. If he or she doesn't, or goes into a tantrum of artistic dudgeon, you should probably consider getting another designer. You can't afford to have a prima donna on your team, frankly. If you and your designer communicate well, he or she works with you to get the best possible solution to the client's needs and is highly creative to boot, you have a jewel. Pamper that designer!
If there is something in a design that doesn't make sense to you, ask why it's that way. You should get a clear, concise and understandable reason why he did it that way. If you don't, it's probably not going to work anyway. If you do, and you don't feel it's valid, say so. If the reason makes sense, you should probably go with it. A designer who understands the project, understands what the end product is supposed to accomplish, will often come up with ideas you may not have thought of. That's where creativity and practicality meet, give each other a quick hug, and get down to business.
So, in a nutshell: Be honest. Communicate. Those two rules will get you out of more difficulties than you would believe.
For future reference, and to help you work with designers as you grow your business, get Robin Williams' "The Non-Designer's Design and Type Books" from Peachpit Press. They will give you the vocabulary and the confidence to know why a design is good or bad, and how to fix it.