Multiple folder scanning no, single folder yes.
For console roms you need No-Intro sets.
For Arcade Rom sets you need the romset matching the cores you have and their version.
To auto scan you just have to highlight the folder and press the left face button [Y/Square/etc.] and it will start the scan process then put that playlist in the main tabs.
Its prety easy to have all the main consoles scanned and easily accessed with picture thumbnails for each game, toggle the thumbnails with the left face button.
CD Console sets require Redump but I'm still a tad confused on those, it appears they require manual outside of RA creation.
It appears with the latest RetroArch nightlies you can now just add folders instead of having to do that tedious process.
I will try to help you with any other info regarding RA as I am the resident RetroArch guru here.