Generally it depends on the mod but there are some key aspects to look for.
A mut is short for mutator, a mut changes some element of gameplay. ServerPerks, NoKillStats, SuperZeds, KillMessages, Nade Warn, MachinePistols etc.
These will have to go into the voting config and start line to ensure they are active on server start and mapchanges but generally don't always need to go into the serverpackages line.
Mods like weapons sometimes come with a mut to implement them but if you are running a mutator like serverperks you only need to add it to the serverperks ini.
You add mods to the serverpackages lines when you need the client to download those files. For example a weapon that doesn't go into ServerPerks will have to be manually added to the serverpackages so that the client will download the assets.
Server Actors are for very specific muts/mods and you should only have to add them to there if instructed to.