When you install 64 bit version of BizTalk sever, the application installation folder will have 2 BizTalk configuration files.
1. BtsNTSvc.exe.config, and
Nowadays most of the production BizTalk servers will be running on 64 bit versions of software (Operating system, BizTalk, SQL etc). In majority of the situation you’ll be only using the 64 bit in-process host instances on the server. In that case all your custom configuration should be placed inside the BtsNTSvc64.exe.config.
But occasionally there will be situations, where you need to run some 32 bit host instances as well on the same servers. Example: If you are utilizing any 3rd party components with 32 bit restrictions, another example :Running the WSE adapter, FTP adapter, SQL adapter, POP3 adapter, and MIME Decoder on 64-bit host instances is not supported (http://technet.microsoft.com/en-us/library/aa560166.aspx). So, you need to run them under 32 bit host instances.
In those scenarios, make sure you copy the configuration data to both BtsNTSvc.exe.config and BtsNTSvc64.exe.config. Because the 32 bit host instances will use the BtsNTSvc.exe.config file.