Adding to what tropic has already done a good job with; think of the FLAC compression levels like what's used by zip, rar, 7-zip, etc... They're all lossless, just finding more bits to compress, thus taking more CPU power and time.

If you're going with a commandline FLAC encoder, which is at 1.1.4, check out the thread started by "gharris" on hydrogenaudio.org. He has posted many compiles of FLAC for various CPU's. Some will possibly cut off a good amount of encoding time with no detrimental effects. It's worth it.