In your start > Programs > Startup folder.. What you put in this folder will run at start up
As for another way to get into msconfig the best way is through run in the start up folder, however if you want to run the risk of having a shortcut on the desktop.
C:windows\servicepackfiles\i386 just look for msconfig and if it,s not there do a search of the C:drive for MSconfig there will be a couple of them right click the one with the red mark on it. Right click it and send it to the desktop.
A way to determine what to have start on startup is if you don't want it to start and it isn't something your video or other hardware need to start then don't have it start. Having programs that you can start manually when you want them in startup will slow down your startup but speed up the launching of that program. StartMan is a good program that does the same thing as msconfig but with a different inferface, and you can have certain programs start for one user and not another. It is a program made by Pcforrest that you install and it controls what starts and what doesn't, just like msconfig.
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MS Config
also how can i determine the programmes to run at start up, other than through msconfig.