FLAC is a lossless compressed format. You should convert them to Apple Lossless Audio File for best result. If you don't have tools to do that, than convert them to AIFF first and than convert AIFF to Apple Lossless in iTunes.
You can also play AIFF in iPad but it will take up more space than Apple Lossless.
You can also play AIFF in iPad but it will take up more space than Apple Lossless.