Moghancement: Nation Conquest and Conquest are the exact same boost to CP gain.
Both have NO effect on IS gain.
The only difference is Nation Conquest only works if you're earning CP for the specific nation, Conquest works no matter who your allegiance is with.
Scenarios:
Moghancement: Other -- CP equal to 10% of XP earned
Moghancement: Windurst Conquest -

Citizen -- CP equal to 16% of XP earned
Moghancement: Windurst Conquest -

/

Citizen -- CP equal to 10% of XP earned
Moghancement: Conquest -

/

/

-- CP equal to 16% of XP earned
I just keep mine on Moghancement: XP full time >.> But I have personally tested the IS gain (stupid Imperial Standard...)