I'm not sure what MusicBee's default FLAC settings are, but they should be fine.
The good thing about FLAC is that being lossless you don't need to tweak a heap of parameters - you're going to end up with a file that sounds identical to what you started with anyway.
One that might be useful is a single number -0 through -8 (-0 being equivalent to --fast, -8 being equivalent to --best). -8 should give the smallest possible file but will take longer to encode. The created files will sound the same - unlike MP3, M4A etc. where a smaller file means lower quality.
Bee excellent to each other...