The Church of Scotland and the Church of England are entirely independent of one another. There are differences in the forms of worship, but the fundamental difference is in how the church hierarchy is organised.
The Church of Scotland is one of many Presbyterian denominations.
Presbyterian churches do not have bishops. the hierarchy is a series of committees. Each congregation is managed by a committee called the Kirk Session, which consists of the minister and elders. Each one sends the minister and representative elder to the Presbytery, which is a committee that oversees a wider area, including all the parishes in that area. Every Presbytery belongs to a still larger area called a Synod, and all Synods belong to the General Assembly, which is made up of all ministers and some but far from all representative elders. Every Presbyterian denomination has its own Kirk Sessions and its own General Assembly so if you are speaking about the 'General Assembly' you should really specify which one - for example the 'General Assembly of the Free Presbyterian Church of Scotland' - but the term 'General Assembly' on its own is usually taken to mean the General Assembly of the Church of Scotland.
The Church of England is one of many Episcopalian denominations. Episcopalian means that the church hierarchy includes bishops.
Apart from one or two small congregations the Church of England does not operate in Scotland. The corresponding Protestant Episcopalian denomination in Scotland is the Scottish Episcopal Church, also known as the Episcopal Church in Scotland, and sometimes referred to as the English Church. It is independent of the Church of England, but is in full communion with the Church of England as part of the worldwide Anglican Communion.