you need to install the database management studio first. then you open the script files in the studio.
it's a bit troublesome when you upgrade from 1.9 to 2.0 because they are using different tables. you need to install 2.0 into 1.9's database without sample data, so both 1.9 and 2.0 tables are residing in same database. then run the 1.9->2.0 script file in management studio.
I agree with nodev did it myself recently. the trick is you have to install nop 2.0 fist to the database before doing the upgrade. this is critical. i did the upgrade before installing 2.0.
then you just use the upgrade scripts on the database until you get to the version you want. once you have upgraded then upload your files and away you go.
hope this helps
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