Thanks for the positive feedback!
1) Note that the Deployment Framework already pushes changes to the BTSNTSvc.exe.config in the areas of debugging options and AppDomain mapping. You may choose to simply overwrite the whole file during your deployment, although if you do that in every
BizTalk app deployment then you could easily end up with conflicting versions of the file. That aside, you can create a target and ItemGroup similar to this:
<Copy DestinationFolder="$(BtsDir)" SourceFiles="..\BTSNTSvc.exe.config" />
I didn't test this but it should be close. I'm assuming here that you have a folder BizTalkConfig under your solution root that contains the BTSNTSvc.exe.config.
2) I guess I'd need to know how you are planning to expose the schemas. Through web services?