Flacs are supported fine. I have a whole library worth of Flacs.
(Even multi-channel and Hires, like 5.1 channel and 192kHz/24bit recordings)
For your particular situation I recommend you to reorder the metadata agents under
Settings - Server - Agents - Artists
and Settings - Server - Agents - Albums
so that 'Local Media Artists' and 'Local Media Albums' respectively are at the top position.
That way the internal metadata of the files get top priority for plex.
Now you must make sure that all your files do contain such internal metadata.
Last time I looked, many if not most files on LMA do not contain metadata and many that do contain them, contain wrong or incomplete ones.
So get them in order. Since you are on Windows, I recommend you mp3tag to edit and add metadata (to both mp3 and FLAC files).
For Plex it is most important to fill in the metadata for an album consistently and to always fill in the 'Album Artist' field with sensible content.
You treat each of your live shows as a separate album of course. So the 'Album' tag for one show must be consistent for all songs within a concert.
If there are guest musicians involved, they can be added to the 'Track Artist', but the 'Album Artist' should only contain the headliner of the show.
(Except, of course, you want this collaboration to appear as a separate 'Artist' in the Artist view of your music library [e.g. Eric Clapton & Mark Knopfler - Beetle Clasher Perfect Soundboard (1989-02-09 Royal Albert Hall)])
Fill in also disc and track numbers (even if these recordings probably never were on disc), just to make sure they are later listed in their right order in Plex.
You can add a jpg file named folder.jpg to each album folder. This will automatically be picked up by plex and be used as cover image for the album.
Embedded cover art is also used by Plex. Just make sure it is of a good quality. Again, you can use mp3tag to edit, erase or add embedded cover art.
If you store your media files on a NAS (that does not use Windows as operating system), you'll want to avoid using file and folder names that contain non-ascii characters. Otherwise, cover art might not be picked up reliably.
Footnote:
I'd personally recommend to only add final cut tracks into plex.
For your master recordings and intermediate mixes to appear in a sensible order, you'd have to metatag these too.
Also, Plex currently doesn't store playback progress for music files. Listening to a whole concert in a single file will be a hassle if you have to pause.
I recommend you to create a separate library for your live music.
You can use 'Personal Media Artist' as primary agent for that library or 'Last.fm'
Last.fm can provide some metadata on the artist and maybe a photo, but if you arrange the order of agents as shown above it will not interfere with the actual tracks (and try for instance to assign track names from a studio album to one of your live recordings).
