Moving from PC to Mac

You can
a. use XLD (free software) to convert all your FLAC to AIFF or Apple Lossless
Both would retain the meta data of the FLAC files. XLD has a setting to "automatically add converted files to iTunes).

b. use something like Pure Music or Audirvana Plus to add FLAC files to iTunes.
This method does not do any conversion. PM/A+ creates a "shortcut" to your FLAC files (in ALAC format) that you can view in iTunes. When you select the file for playback, PM/A+ works in the background to dynamically play the FLAC file using its own playback engine (which is superior to iTunes')

Method b means that the generated files don't work when you sync it with an iPod or iPhone etc though. But if this is for a music server, it should be fine.

I recommend Audirvana Plus as it also plays DSD files, sounds great and is cheaper than most of the other options (last time I checked). I have PM and Amarra as well (having bought Amarra when it was over 500 bucks! so I think I am unbiased here).

I got downloaded flac files, I am on mac. I simply downloaded an app from itunes store, it costs 9.99 and it converts any format to any other.It does it super fast. All you do is drag the files to be converted into the music converter opened Window choose destination drive, in my case it's an external usb drive, and click convert.Simple,fast,reliable.I personally found XLD clunky.
Regards
George

Why convert the files? Use Cog for playing back your flac files on a Mac.

I use XLD also because it has an EAC-type ripper for CD ripping.

I use iTunes to manage my music library that I use for music server functions as well as syncing with my iOS devices

So conversion is needed.

If I am not running headless (ie when using a notebook with keyboard/mouse rather than a Mac Mini), I tend to use Audirvana in Playlist mode which can play DSD, ISO and FLAC files directly without conversion.

I dunno about COG but A+ sounds superb

Some recommendations:

http://www.empiricalaudio.com/computer-audio/recommended-systems

Steve N.
Empirical Audio

I just went through this and found that Pure Music sounded best to me in my system. I think the player may be somewhat dependent on the DAC used since with my NOS HEX DAC I am not able to use Audirvana in integer mode so I may not be hearing that player at its best. Thanks to a tip from Srajan of 6moons, I am upsampling at the player to 176.4kHz using Pure Music set to NOS.

Install Windows 8 pro on the Mac mini.