I am not sure I am understanding what you mean by a "small" trachea. Bostons are what is known as brachycephalic, which means short wide head. Because of the formation of their head they are more prone to respiratory issues, such as an elongated soft palate, or tracheal stenosis which is a narrowing of the trachea. Do you remember the exact term your vet used?
Most people with breeds that are brachycephalic, like Boston's, Pug's, and English bulldogs, have to take extra precautions when it is hot out because these breeds can overheat very quickly. If you can keep a baby pool in your yard filled with water that can help them keep cooler when it is hot out. Air conditioning is also a must for these breeds. As far as breathing difficulties I would not allow them to play too long or too hard. As soon as you notice them starting to have difficulty breathing stop play and allow them to rest.
Did y our vet mention anything about a Collapsing Trachea? That is not specific to Brachycephalic breeds, just small breeds in general. A Collapsing TRachea is just that, pretty self explanatory. You will usually notice that after exercise a dog will "cough". In extreme cases, rings can be placed surgically in the trachea to help prevent it from collapsing. Generally speaking the majority of dog's do not have it so bad where surgery is necessary. Owners with dogs like this should never use a collar to walk their dog. A harness is much better for them as if they should pull it is not causing undue pressure on the trachea and exacerbating the problem.