I've read that James I & VI had some trouble early on in dealing with the English parliament, because he was used to a Scottish parliament that was mostly a rubber stamp. But I've also read that Scotland was pretty independent from England before the Acts of Union, and that the monarchs were mostly forced by their courts to stay in London.
So who was actually in charge in Scotland? Was the Scottish parliament more of an independent body than I had been led to believe? Did it reassert its independence in the absence of the King? Or was there some other power like a regency?
The situation varied at different points, but in theory the King's representative in Scotland was the 'Lord High Commissioner'. In effect, this was the head of government in Scotland, although there was also a 'Lord Chancellor' who held the role nominally.
However, Scotland also had a Parliament and a 'General Assembly' of it's Kirk (church), and both these bodies exercised varying degrees of power at different points.
Essentially, from 1603-1638, the monarchy ruled Scotland via Lord High Commissioners, though this did not always mean they could do anything they wanted, as the powers of Scotland's monarchy were somewhat more limited than England's.
In 1638, the Scottish General Assembly drew up a 'National Covenant' for resisting changes to their religion that Charles I sought to impose, and the Scottish Parliament adopted it in 1640. It was, in several respects, a de facto declaration of independence, although in theory the Scots professed they remained loyal to the king.
Various factions of 'Covenanters' would then govern Scotland until 1651, when Cromwell conquered the kingdom and absorbed it into the Commonwealth.
After 1660, when the monarchy was restored, the system returned to being dominated by Lord High Commissioners, though this position in the Restoration period was a very difficult one, with those who filled it unable to balance the demands they faced from England with the reality of the situation in Scotland.
The Scottish parliament gained more powers after the Revolution of 1688, though not as much as it had enjoyed in the Covenanter period, and the Lord High Commissioner remained an important role until 1707.