Autonomy IDOL with a bunch of fetches (especially the file system fetch/connector with a pair of security services each) can amount to a painful deployment when it comes to configuring the Windows Services.
When everything is installed, you can turn to sc.exe (part of the OS in Windows Server 2003, used to be in the Resource Kit) to help automate the credentials change:
Note that the space after the equals is important. You can also set the startup type with:
A bunch of these in a script can help immensely with deployments. Run sc.exe by itself on the command-line to see a number of other powerful options (including controlling remote services).