BizTalk uses its own configuration file called
btsntsvc.exe.config which is in the BizTalk program files directory. You can
add your configuration sections into this file and then bounce the biztalk host
instances to pick up the changes.
HOWEVER, this is not good practice. It's OK to do this when
you have only a single BizTalk app server but if you need to scale out suddenly
you have multiple config files to maintain.
The recommended approach is to use SSO to store app-specific
Config data, since it's BizTalk's Config storage solution and therefore always
available. I always use this method and have never had any problems (although
there is some overhead associated with development and management).
Ref: http://stackoverflow.com/questions/10107460/call-net-assembly-from-biztalk-orchestration-where-to-put-confighttp://seroter.wordpress.com/2007/09/21/biztalk-sso-configuration-data-storage-tool/
http://geekswithblogs.net/paulp/archive/2008/05/16/122205.aspx
http://geekswithblogs.net/paulp/archive/2008/06/09/122746.aspx
http://stackoverflow.com/questions/11744571/store-configurable-values-in-sso/11746059#11746059