Here is a brief example of PeX group setups. You can look up the additional permissions nodes you need for certain plugins and add them as displayed below. Same format.
groups:
Default:
default: true
options:
rank: '1000'
prefix: '&7'
suffix: ' &8[Guest]&f'
permissions:
- -modifyworld.blocks.(place|destroy).*
- -modifyworld.vehicle.destroy
- essentials.motd
- essentials.help
- essentials.info
- essentials.rules
Mod:
options:
rank: '0'
prefix: '&7'
suffix: ' &5[Mod]&7'
inheritance:
- Member
permissions:
- modifyworld.*
- essentials.togglejail
- worldguard.string
- essentials.ban
- essentials.mute
- essentials.unban
Admin:
options:
rank: '0'
prefix: '&7'
suffix: ' &4[Admin]&f'
permissions:
- '*'
Owner:
options:
rank: '0'
prefix: '&f'
suffix: ' &b[Owner]'
permissions:
- '*'