No, not too much difference unless you're looking to spend lot's of money and are looking for serious detail.
A 3-way speaker generally can play lower and deeper than a 2 way speaker since it has has 3 drivers, one Tweeter for the highs, a mid-range for all of your mid frequency sound, and a woofer for your low frequency sound. A 2 way speaker will generally have one tweeter and one mid/woofer combo. The
frequency response of your subwoofer is what you want to find out. If your subs frequency response is say: 35hz - 100hz, and lets say you find L/C/R speakers that have a frequency response of 68hz-20,000hz (aka-20khz), it won't matter so much if the speakers are 2 way or 3 way. Be sure to have your crossover setting as 80hz. If you cannot access the crossover setting, it is common for the factory to preset the the crossover to 80hz. The crossover will send all of the sound below 80hz to be played only on the subwoofer and anything above 80hz to your L/C/F's. This way, you are enabling each speaker to reproduce the sound it is capable of. Make sure you select small as the speaker size setting when setting up your system.
