Fourier decomposition allows you to take any function of time and describe it as a sum of sine waves each with different amplitudes and frequencies. If however you want to approach this problem using the DFT, you need to make sure you have sufficient resolution in the frequency domain in order to distinguish between different frequencies. Once you have that you can determine which frequencies are dominant in the signal and create a signal consisting of multiples sinewaves corresponding to those frequencies. You are correct in saying that with a sampling frequency of 44.1 kHz, only looking at 256 samples, the lowest frequency you will be able to detect in those 256 samples is a frequency of 172 Hz.
OBTAIN SUFFICIENT RESOLUTION IN THE FREQUENCY DOMAIN:
Amplitude values for frequencies "only at certain frequencies, multiples of a base frequency", is true for Fourier decomposition, NOT the DFT, which will have a frequency resolution of a certain increment. The frequency resolution of the DFT is related to the sampling rate and number of samples of the time-domain signal used to calculate the DFT. Reducing the frequency spacing will give you a better ability to distinguish between two frequencies close together and this can be done in two ways;
- Decreasing the sampling rate, but this would move the periodic repetitions in frequency closer together. (Remember NyQuist theorem here)
- Increase the number of samples which you use to calculate the DFT. If only the 256 samples are available, one can perform "zero padding" where 0-valued samples are appended to the end of the data, but there are some effects to this which needs to be considered.
HOW TO COME TO A CONCLUSION:
If you depict the frequency content of different audio signals into individual graphs, you will find that the amplitudes differ abit. This is because the individual signals will not be identical in sound, and there is always noise inherent in any signal (from the surroundings and the hardware itself). Therefore, what you want to do is to take the average of two or more DFT signals to remove noise and get a more accurate represention of the frequency content. Depending on your application, this may not be possible if the sound you are capturing is noticably changing rapidly over time (for example speech, or music). Averaging is thus only useful if all the signals to be averaged are pretty much equal in sound (individual seperate recordings of "the same thing"). Just to clarify, from, for example, four time-domain signals, you want to create four frequency domain signals (using a DFT method), and then calculate the average of the four frequency-domain signals into a single averaged frequency-domain signal. This will remove noise and give you a better representation of which frequencies are inherent in your audio.
AN ALTERNATIVE SOLUTION:
If you know that your signal is supposed to contain a certain number of dominant frequencies (not too many) and these are the only ones your are interesting in, then I would recommend that you use Pisarenko's harmonic decomposition (PHD) or Multiple signal classification (MUSIC, nice abbreviation!) to find these frequencies (and their corresponding amplitude values). This is less intensive computationally than the DFT. For example. if you KNOW the signal contains 3 dominant frequencies, Pisarenko will return the frequency values for these three, but keep in mind that the DFT reveals much more information, allowing you come to more conclusions.