.Net apps are very, very strict in their PE layout and structure. I doubt you can reliably connect your own section on to a .NET PE file. It would be better to make a normal launcher EXE, and then embed the .NET app into that in a new section, and use reflection to launch it from memory.

I'm assuming you have read thru the ECMA specs for .NET PE structures. It does make notes like required section alignment, etc. From my experience it is really not possible to modify a .NET PE file in "old" ways of how most protectors work - once you do so, the .NET program will not run.

-Lunar