Complex sentence: However, political and military realities led to greater influence for the congregational party, which favoured autonomy for individual congregations rather than the subjection of congregations to regional and national assemblies entailed in presbyterianism.
Split into simpler sentences: However, political and military realities led to greater influence for the congregational party. Congregationalists favoured autonomy for individual congregations rather than the subjection of congregations to regional and national assemblies entailed in presbyterianism.