List of all badges with full descriptions
I want to know what "Raised 80 helpful flags" means. Should I flag 80 comments, or what?
It means that at least 80 flags you raised were deemed helpful by the moderator(s) that handled them. There are some instances where a flag is automatically deemed helpful, for example if you flag a question as Off Topic and then a 3K+ user votes to close it as such.
Since you brought this up in the context of the deputy badge, you should keep in mind that flags are (mostly) handled by moderators, and if you go around mindlessly flagging just to get a badge, you may get in trouble.
As for the side question on whether comment flags count towards the deputy badge, well here's my flagging history on The Workplace:
Obviously I couldn't have gotten the badge if comment flags didn't count, but here it is. ;)
Flags aren't meant only for comments. You can flag questions,answers,users(who does nasty things like voting fraud) and also comments. Those flags are only counted when they are helpful. A moderator should approve that those flags helped in some way!