To change the setup for a scenario, go to the scenario folder and find the right scenario. In that directory, you'll see files with an INC extension. In each of those is a setup of a country.
For example, a portion of the fiile prussia.inc in the 1836 scenario looks like the text below. You can change the settings and when you start the scenario, poof, things are different. Note that the party is the ID of the party in that nation's party file.
ruling_party = 4608
voting_rights = none
press_rights = state_press
political_parties = right_to_ban
trade_unions = none
public_meetings = yes
maximum_workhours = 0
minimum_wages = none
safety_regulations = none
health_care = none
unemployment_subsidies = none
pension_funds = none
government = monarchy
executive_designation = laws_by_decree
establishment = traditional_academic
party_system = two_party
national_value = order