You need to have the correct xml files within the hyperspin\database\mame folder. If you have the latest 145 set of roms then when at home page of hyperspin click on hyperlist you can download the xml file for .145 ongoing (It may be worth getting this xml anyway).
I used a program called HyperSpinXMLBidouilleur.exe to create a modified xml file that only lists the games that I have.
Basically get hold of the above, run it, select roms, Then you can select mame, point it at your mame roms folder.
Click on analyze and it will show you all your games along with whether its a clone and various other information.
You can then create an xml file or update an existing one.
Hyperspin uses xml for pretty much everything. If you plan on using it for multiple emulators then read read read is all I can advise. There are many
tools to make your life easier, the above program along with HyperSpin_RomManager.exe should get you an xml file that only lists the games you have (With or without clones, depending on your choices).
All your roms should be in one folder (I stuck mine in hyperspin\roms\mame) and they should all be .zip files, both mame and hyperspin need to know the location of these roms to do anything properly

There should be no need to create individual folders or anything (unless there is a chd file required).
Hope this helps you along a bit.