Assuming you don't want to replace your FLACs with MP3s, and you don't want to put them in the same folder as the source file, I'd suggest setting the options in Tools/Convert Format.
Select the 'or to a new folder option'
Set to root path for the MP3 files
Configure the creation of artist and album names from the metadata tags: 'organise sub-folder and filename'. The default configuration is sensible, assuming you already have files organised as AlbumArtist/Album/Title.
<Album Artist>\<Album>\<Disc-Track#> <Title>