When you upgrade from BizTalk 2004 to BizTalk 2006, MSMQ adapter is installed by default. If you had MSMQ/T adapter enabled in 2004, it will also be enabled after you upgrade to 2006. You’ll see the MSMQ adapter, but it won’t be doing anything. The adapters don’t conflict with each other and you can have both installed without any problems. The conflict would be between BizTalk with MSMQT and the Windows MSMQ service. As long as the MSMQ service is not running, you will not have problems.
Though MSMQ/T is fully supported in BizTalk 2006, if you want to migrate to MSMQ somtime in future follow the steps mentioned in Migration considerations for moving from MSMQ/T to MSMQ adapter in BizTalk 2006