There are 2 locations to store SSIS packages: The file system or SQL Server. The rest is semantics.
File System
You can use the SSIS Package Store which is nothing but a well known location in the installation location.
%Program Files%\Microsoft SQL Server\{Version}\DTS\Packages
Or you can pick anywhere on the file system you like. If you go this route, then you'll need to ensure the SQL Agent account, or the credentialed proxies or, if you running packages from xp_cmdshell the SQL Server Service Account has access to that location.
The only advantage, if you want to call it that, of using the Package Store (i.e. the folder I mentioned) is you can use the Integration Services management tool that exists in SSMS (by connecting to Integration Services instead of database engine).

However that has a lot of pitfalls such as not being able to handle multiple instances, packages only run in 64 bit mode, no access to proxy accounts, etc. You shouldn't run packages from SSMS anyway.
SQL Server
If memory serves correct
- 2005 - stored in msdb.dbo.sysdtspackages90
- 2008 - stored in msdb.dbo.sysssispackages (I seem to recall 2008 RTM using a different table, or reused the 90 table but that got patched out)
- 2008 R2 - stored in msdb.dbo.sysssispackages
- 2012 (package deployment model) - stored in msdb.dbo.sysssispackages
- 2012 (project deployment model) - stored in SSISDB.catalog.packages*
- 2014 (package deployment model) - stored in msdb.dbo.sysssispackages
- 2014 (project deployment model) - stored in SSISDB.catalog.packages*
*With the project deployment model, packages are "compiled" (zipped with a manifest) into a .ispac which is stored into the bowels of the SSISDB.internals.* tables.
Wrapup
Ultimately, where you store your packages does not affect your ability to run them. You can run packages using DTEXEC, SQL Agent or custom .NET code. The choice of storing packages is primarily dependent upon your management style.
References
You can make the package connection configurable.
- select "SSIS">> Pacakage Configuration >> navigate to connection >> select servername and database name
- Click next
- Save pacakge configuration to dtsconfig file.
During deployment modify this dtsconfig file and specify.
Best Solution
For Latest Info About SSIS > https://docs.microsoft.com/en-us/sql/integration-services/sql-server-integration-services
From the above referenced site:
Getting Started with SSIS - http://msdn.microsoft.com/en-us/sqlserver/bb671393.aspx
If you are Integration Services Information Worker - http://msdn.microsoft.com/en-us/library/ms141667.aspx
If you are Integration Services Administrator - http://msdn.microsoft.com/en-us/library/ms137815.aspx
If you are Integration Services Developer - http://msdn.microsoft.com/en-us/library/ms137709.aspx
If you are Integration Services Architect - http://msdn.microsoft.com/en-us/library/ms142161.aspx
Overview of SSIS - http://msdn.microsoft.com/en-us/library/ms141263.aspx
Integration Services How-to Topics - http://msdn.microsoft.com/en-us/library/ms141767.aspx