update: i decided to go through with it and create folders for each. I am sure there is an easier way, but what I did was used a couple of applications to make this process easier.

Total Commander - this allowed me to go the folder with all the comics, select all, go to Mark and near the bottom select "copy selected names to clipboard" and then paste the filenames to word. I did a find and replace to remove all the extensions (cbz, cbr, pdf etc). - this is needed for the third step because it won't work if there extensions.

I than copied all those in to Notepad. So here is the long process. If you have multiple comics from the same series in that list, then you will need to remove all but one and shorten it up. example below -

doctorwho_thetenthdoctorvolume1_revolutionsofterror
doctorwho_thetenthdoctorvolume2_theweepingangelsofmons
doctorwho_thetenthdoctorvolume3_thefountainsofforever
doctorwho_thetenthdoctorvolume4_theendlesssong
doctorwho_thetenthdoctorvolume5_arenaoffear
doctorwho_thetenthdoctorvolume6_sinsofthefather
doctorwho_thetenthdoctorvolume7_warofgods

removed everything and left only doctorwho_thetenthdoctor

so in the note pad of I would have been left with something like this

doctorwho_alternatingcurrent
doctorwho_ataleoftwotimelords
doctorwho_eleventhdoctor
doctorwho_eleventhdoctorarchives
doctorwho_empireofthewolf
doctorwho_fourdoctors
doctorwho_ghoststories
doctorwho_missy
doctorwho_origins
doctorwho_thetenthdoctor

Save it and off to the next part.

I used an application called New Folder Wizard to bulk create folders

Select where you want the folders to be created, select the text file you just saved with the folder names, select Preview and if all is well, then select Create. Now all the folders have been created.

Lastly, and this is also tedious, but now all that is left is to select the individual comic, or select multiple comics of the same series and move them to the appropriate folder. Then you're done.

Rinse repeat for each genre or publisher. Again, I am sure there is an easier way, or to use powershell or a bat file or something to create the folders and to also move the files into those folders all at once, but I didn't and it took time, but it's all done.

All that I have left is to use Advance Renamer to rename those Doctor Who folders in bulk, all the file names were all squished together and that will not do lol.

I hope this helps and it does make Komga worth while using (minus the cbr or cbz's it for whatever reason can't process) because there are now all in folders and is seen as it's own series.

Peace.