You only need to follow the offical storing method which is always the same for all collections:
rompath\setname\file 1...file n for decompressed sets or rompath\setname.zip (.rar/.7z) from compressed sets (where the archive then holds the single files)
The marquee dat (and actually most of the progetto collections) uses 1 set with some thousand files in it (the single pngs), so when you e.g. use e:\progretto\the_marquees as your rompath, your stored files should look like:
e:\progretto\the_marquees\marquees\3b1.png .... zzyzzyxx2.png or e:\progretto\the_marquees\marquees.zip (.7z/.rar) with 31b1.png....zzyzzyxx2.png in the archive root level. Make yourself clear what the rompath and what the setname is. If you got that, it's easy.
Additionally it's recommended to turn off fix-missing (and my personal taste: keep the pngs decompressed)
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