The Scottish National Party (SNP) chose to proceed by forming a minority government. This entailed governing via negotiation and garnering support from other parties on each single policy. Passing annual budget statements became difficult due to constant, competing demands for various amendments. It was also possible for the Parliament to pass opposition motions. In this fashion, the design of the Parliament effectively blocked nationalist 'control', with the second, third and fourth largest parties all being unionist, in a co-aligned majority on the constitution.
A problem faced by both the SNP and Labour, however, was cohabitation. This term came from France, where it had been possible for the two most powerful institutions to be held by opposing politicians – the President could be conservative while the Parliament was socialist. The concept was applied to Scotland in so far as Westminster was controlled by New Labour and Holyrood by the SNP. Between 1999 and 2007 Labour had effective control over both parliaments, and their coalition partners in Scotland (the LibDems) were not only pro-union but 'centre left' in political outlook, thereby making cohabitation an irrelevant concern. Indeed, prior to 2007 concern about cohabitation was focused on the possibility of a Labour government in Holyrood dealing with a Conservative one in Westminster.
Take your learning further
Watch a short video by Glenn Campbell entitled SNP: From Protest to Power which sums up the journey travelled by the SNP over its 70 year existence. You can also read a news report on Scottish minority government.