It is always a pain to convert cue+flac files in Linux. Most methods are done in command line. This is until I found Flacon. A GUI tool that can split a FLAC file into tracks and convert them into a desire format.
You can either get the software from its main site (https://flacon.github.io/) or from PPA (https://launchpad.net/~flacon/+archive/ubuntu/ppa)
