Full Article here:  http://social.technet.microsoft.com/wiki/contents/articles/35656.biztalk-improve-deployment-and-tracking-by-always-creating-custom-pipelines.aspx

While the Default Pipelines are functional and perfectly fine for testing or experimental purposes, we should always create and deploy custom Pipelines for all Ports used in our apps, even if they are same composition as the default Pipelines. There are a number of reasons to take this minimal extra step. First, and relatively minor is that the Tracking settings for the default Pipeline are turned off by default. This has led to a number of questions on the Forums about “missing messages” or “BizTalk not working”. The reality is that the app is running normally, but no tracking data is being written. The solution is simple, enable Tracking, but it’s an all or nothing scenario with the default pipelines. Next, using custom Pipelines makes Tracking readable and understandable. Finally, this is only* way to eliminate any current and future Schema resolution errors raised by the XmlDisassembler or XmlAssembler. I have rule, all XmlDisassembler and XmlAssembler component must be configured specifically with the Envelopes and Documents they are expected to process. Relying on the default global resolution is forbidden. Working With the Sample Project The sample Visual Studio Solution can be downloaded from: Note, Deployment Units for Production Applications should be maintained at the Solution level. The sample project uses single Solution for demo purposes only. The Solution contains a .zip of the c:\ drive folder. Build and Deploy the Solution. Only ProjectA and ProjectB will Deploy. ProjectA_Pipelines is set to now Deploy. At this point, you can copy the sample file to any of the receive folders to see the pipeline use. One ProjectA Receive Location will fail because of duplicate Schemas. Build ProjectA_Pipelines and add it to ProjectA. Set the Pipeline on TradingPartnerOneReceive to the new, side-deployed Pipeline. Cope the test file again. No error is generated.