FLAC is lossless compression, as long as your playback hardware supports it, then it is recommended.
For loading portable mp3 players or burning an mp3 disc, when space is limited and sound quality is not as crucial, you can get a media manager program that will compress to mp3 (or other format) on the fly without altering your FLAC collection.
EAC is free, but I found dbPoweramp to be a real timesaver worth the money. Much easier to tag. They both use Accuraterip, so if your rip is bit-perfect, no matter the speed, settings or program used, then Accuraterip will tell you. The default settings can usually do this. The more complicated settings reserved for the occasional problem disc. You can also try EAC on the problem discs to see if you get better results.