There isn't really a "good" way to design a base, because it depends a lot on the player and what they like. That's the whole point of Minecraft: You can do things however you want, especially when it comes to building.
If you're not a creative person in this sense, building underground might be a good alternative, because you don't have to think about how things look from outside, and using various combinations of different kinds of stone is likely to look good. Another tip is, if you're tired of cubes, make your buildings with rounded corners. It's not hard, and you'de be surprised at how much better things look. But if you really want desiging and building advice, you should take this to another forum, since your question doesn't have a lot to do with Feed The Beast specifically.
If, on the other hand, you're having trouble coming up with a good way to arrange your base so it's easy to mantain a big network of machines, pipes and whatnot, then your best bet is probably building underground, because you've got unlimited room for expansion and it's easy to move things around. For example, in my world the main buildings (storage, ore processing, farms, etc.) are above ground, but the power generation is in a big square basement, and my pipes and cables all run below ground.
