1. A method of protecting a configuration bitstream, the method comprising: encoding at least a portion of a configuration bitstream using a first key to generate an encoded configuration bitstream; storing the encoded configuration bitstream in a first memory on a first integrated circuit; receiving, at a first circuit of a second integrated circuit, the first key, wherein the first key is received at the second integrated circuit from a source external to the second integrated circuit; obfuscating, with the first circuit, the first key to generate a second key; and storing the second key in a second memory on the second integrated circuit, wherein the second memory is a non-volatile memory.