Here's an example command line using the naming convention of Visual Studio 2005, where the manifest filename contains the program name with ".intermediate.manifest" appended.
mt.exe -nologo -manifest "program.exe.intermediate.manifest" -outputresource:"program.exe;#1
And now for a story...
When we were first confronted with the need for manifests - specifically for triggering UAC prompts in our configuration tools written in VB6 - I performed my due diligence. I researched the topic thoroughly, I took examples of the manifests provided by Microsoft, and I tested on each and every Windows OS we supported - Windows 2000 all the way up to Windows Vista/2008.
The one thing I couldn't find was a simple way to embed the manifest in those executables, that could be easily automated. The articles I read covered GUI tools like XN Resource Editor and Resource Hacker, writing my own C/++ program using UpdateResource, a long winding route using the Resource Compiler (rc.exe) or finally just leaving the manifest as a separate file.
Even though manifests had been around since Windows XP, there wasn't a single article I could find that even mentioned the Manifest Tool. Even in the Microsoft articles I have found, there is never any mention of VB6 and the Manifest Tool together. Of course, VB6 was considered legacy by the time Application Manifests came out; so, while frustrating, I can't really blame them. I can blame my search engine skills, but that's no fun.
Anyway, all but the last option were complicated, convoluted, or required too much effort. We, of course, finally settled on that last option - using external manifests - out of necessity to get something out the door. It wasn't until we started migrating code from Visual C++ 6.0 over to Visual Studio 2005 that I noticed the mt.exe command line in the build log, which was over a year and half later. Now, along with code signing, through signtool.exe the Manifest Tool is included in much of our automated build process, and I am much happier for discovering it.