Like the Confederate Flag, the crosses are arranged as a Scottish St. Andrew's Cross. The Scottish link can be traced to an American priest, Samuel Seabury, who was consecrated bishop in Aberdeen at the Episcopal Church of Scotland in November 1784.
Scotland was, by that time, part of Great Britain, yet Seabury did not have to swear allegiance to the British Crown. This was because when the Catholic King James II was deposed in the Glorious Revolution of 1688, the bishops of the Episcopal Church in Scotland refused to swear allegiance to the new monarchs William and Mary. Swearing allegiance was for life.
As a consequence, the Presbyterian Church was made the official Church of Scotland. The Episcopal Church of Scotland was disestablished and no longer officially recognised by the State. Therefore it was not necessary seek permission from the Parliament of England to consecrate Seabury, and Seabury was not required to reciprocate with any display of loyalty to the Crown.
Even so, Seabury was a loyalist at heart and this made him unpopular to some when he returned to America. But he had strong support from the majority of the New England clergy and became the Church's first Archbishop
The nine dioceses convened in Philadelphia in 1789 and adopted the Constitution of the Church with a House of Bishops, a House of Clerical and Lay Deputies, and the Book of Common Prayer. Today, some congregations still use the 1928 Book of Common Prayer of Scotland.