Can you please elaborate on what you mean by "application server" in this context
If you're storing the DTSX package files on the file system, it probably makes sense to do the same with your config files. Store them as dtsConfig XML configuration files, ideally as "indirect" XML file configurations, where the fully qualified path to the files are stored in Windows environment variables. This should give you all of the flexibility you need.
To execute the packages from the file system, use the DTEXEC command line utility. The easiest way to do this is to use the DTEXECUI utility to build the command-line parameters for DTEXEC. It's much easier than doing everything yourself by hand.