How Do I Configure SSIS to Work With a Named Instance? 

By default, SSIS (SQL Server Integration Services) uses the msdb database of the default instance on the server for storing packages. SSIS can still manage packages stored as files in the file system without any changes to the current setup. To be able to use the msdb database of a named instance, you have to manually edit the SSIS configuration file. Here are the steps for that:

1. Shut down the IS service
2. Find the configuration file: <install location>\Microsoft SQL Server\90\DTS\Binn\MsDtsSrvr.ini.xml
3. Open the configuration file in a text editor such as Notepad
4. To configure a named instance instead of the default instance, change the existing ServerName entry to ServerName\InstanceName under the Folder node of type SQLServerFolder
5. To configure a named instance in addition to the default instance, add a new Folder node of type SQLServerFolder under the TopLevelFolders node
6. Save and close the configuration file
7. (Re)start the IS service

Before change:

<?xml version="1.0" encoding="utf-8"?>
<DtsServiceConfiguration xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
 <StopExecutingPackagesOnShutdown>true</StopExecutingPackagesOnShutdown>
 <TopLevelFolders>
  <Folder xsi:type="SqlServerFolder">
   <Name>MSDB</Name>
   <ServerName>.</ServerName>
  </Folder>
  <Folder xsi:type="FileSystemFolder">
   <Name>File System</Name>
   <StorePath>..\Packages</StorePath>
  </Folder>
 </TopLevelFolders> 
</DtsServiceConfiguration>

After change to a named instance:

<?xml version="1.0" encoding="utf-8"?>
<DtsServiceConfiguration xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
 <StopExecutingPackagesOnShutdown>true</StopExecutingPackagesOnShutdown>
 <TopLevelFolders>
  <Folder xsi:type="SqlServerFolder">
   <Name>MSDB</Name>
   <ServerName>MyServer\Myinstance01</ServerName>
  </Folder>
  <Folder xsi:type="FileSystemFolder">
   <Name>File System</Name>
   <StorePath>..\Packages</StorePath>
  </Folder>
 </TopLevelFolders> 
</DtsServiceConfiguration>

1. Component Services -> Computers -> My Computer -> DCOM Config -> MSDTSServer
2. Right click on MSDTSServer
3. Click properties
4. Click on the Security tab
5. Select Customize and add the users/groups to the Launch/Activation and Access tabs accordingly
6. Add the user to the local Distributed COM Users group
7. Restart the SSIS service