If you are using SSIS 2012, you should also be aware of the new project deployment model. Some fairly detailed info here
If you use it, you don't get any choice about the location of the packages (they go into SQL Server - a new database called the SSIS Catalog). You will find lots of resources on-line regarding pros and cons of using it. For me, there aren't many cons, though it takes a while to get used to the idea that single packages can no longer be deployed in isolation, if you're familiar with the pre-2012 way of doing things.
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