In a convent, what's the difference between a Mother and a Sister?

“Mother” is a “Sister” with seniority and supervisory and administrative responsibilities.

Can a convent have more than one mother? Isn’t the top gun the Mother Superior?

In the Catholic Church, a nun is a woman who has taken solemn vows (the male equivalent is often called a monk or friar). The main distinction between a nun and a sister is that nuns have solemn vows and sisters have simple vows, which allows them to inherit property, unlike a nun. A nun who is elected to head her religious house is termed an abbess if the house is an abbey or more generically may be referred to as the Mother Superior and styled “Reverend Mother”. Wikipedia

It is different for nuns of different faiths such as Buddhism and Eastern Orthodox.

@gailcalled The mental image invoked by your use of the tern “top gun” sent me rofl.