I have a 2008 server that has 3 named instances. So it has 3 data engines, 3 job agents - but only 1 Integration Services service.
To be able to run an SSIS package against any of the 3 instances -- would I have to build 3 separate packages and in each one reference the appropriate connection manager that would point to that db instance? Any other way?
nope. you just have to create single SSIS package and store in file system. then call it from sql serger agents on 3 instances to execute. if it needs to access data from any of db make sure you make configuration items for connection manager connection string properties and set correct values from the sql jobs
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