In most situations you should be able to install fiber board along wood siding without too much trouble. Installing fiber board over wood siding is not usually possible, but if you want to keep one wall as wood and one wall as fiber board, or only use one material along the top or bottom of the house, you should be fine. However, wood is not nearly as durable as fiber board and when it starts to wear down, the differences will be noticeable.
When first installed you shouldn't need to worry about the appearance between wood and fiber board. Look for cement-based siding that has been designed to mimic the pattern and look of wood siding, preferably in the right color (although painting is usually an option). Both fiber board and wood siding are usually installed in the same type of overlapping pattern.
When installing fiber board siding, some elements are made of wood. For example, the water table trim on the bottom of the house can be made of wood to help save on costs. The frieze board, installed right below the soffit, can also be made of wood. Although not true siding, plywood supports are often used around corners and angles when working with fiber board siding.
You will probably need to paint your fiber board siding within several months after installing it. Choose the same color of paint for both your wood siding and fiber board, preferably an acrylic latex exterior paint. This is one area where matching the two materials might pose a challenge, because the paint will adhere differently to either siding and may flake off the wood more quickly over time.