Using BTSNTSvc.exe.config to store the AppSettings value for BizTalk is a common practice.
We can use a separate file to store these values.
This can be achieved by following the steps below
1. In the appSettings element set its file attribute to the filename which will contain the appSettings
<add key="WriteToDebugView" value="true"/>
2. Create the MyFileName.Config and store the content as follows
<!– Common settings for all applications –>
<add key="ConnectionString" value="Integrated Security=SSPI;Data Source=MyDS;Initial Catalog=MsgBoxDb" />
<!– Settings for My Orchestration –>
<add key="DEBUG_FLAG" value="true"/>