Are there many masculine nouns with feminine endings?
Not many, but there are some masculine nouns that are used a lot:
мужчина, папа, дедушка
Almost all of Russian male names have feminine endings in their short version:
Александр - Саша
Михаил - Миша
Григорий - Гриша
Николай - Коля
How are masculine nouns with feminine endings declined?
They are declined like feminine nouns according to their endings.
В комнате нет папы (Genitive) = Dad is not is not in the room.
Женщина разговаривает с мужчиной (Instrumental) = A woman is talking with a man.