This is a rather basic question that does not really belong into this thread. You also failed to provide details on which product you mean. Please check here before posting the next question: http://www.catb.org/~esr/faqs/smart-questions.html

I assume you are not talking about BFL minirig, but other products. They are connected to a computer via USB and you need a mining software on the computer to use them. The mining software communicates with the pool over the network (or with bitcoind when mining solo), and uses the BFL hardware to solve cryptographic tasks. The BFL hardware is not aware of what protocol your software uses, it just crunches numbers as directed by the software. You should check which protocols are supported by the mining software of your choice. You will find that both stratum and getwork are supported by practically all the miners.

Make sure you read up on the topic - you could save yourself some frustration/headache.

Cheers,
   T