Here are the six clauses:
1. That no religion shall be established by law;
2. That no preference shall be given by law to any religious sect, society, denomination, or mode of worship;
3. That no one shall be compelled by law to attend any place of worship;
4. Nor to pay any tithes, taxes, or other rate for building or repairing any place of worship, or for maintaining any minister or ministry;
5. That no religious test shall be required as a qualification to any office or public trust under this state;
6. And that the civil rights, privileges, and capacities of any citizen shall not be in any manner affected by his religious principles.
All concern specific injunctions against the state from becoming entangled in the operations of organized churches, and injunctions against curtailing rights.
In this context, the preference mentioned in the second clause could be e.g. a law that exempts only Baptist churches from paying property taxes, or accords Lutherans representation in the legislature, etc.