dBpoweramp has a batch converter that would do the whole lot at once, posting the FLAC files into individual folders for each album (with Replay Gain etc). There is a free full functionality trial but I suspect most people on this site who use it have happily paid for a full license, I have and I mainly use Macs.

MP3Tag will get you metadata from a variety of specifiable sources and write them to FLAC files. dBpa has similar functionality.

For multi disc sets I usually check and double check the disc numbers are right in Sooloos before importing. Correct disc number metadata does not usually guarantee that Sooloos picks up this nuance, and I find I usually have to do a separate data save for disc number (ie I edit disc numbers only, save data in Sooloos, then edit any other metadata separately before importing).

Sooloos, Roon, G series (with LPS upgrade), 800 series (with LPS upgrade), HD621, AC200, Prime and PS, DSPs old and new.

Purdeys, Moke, Leica, 'Blad. Only the best.