Can you help me to configure the Apple keyboard in Microsoft Remote Desktop Connection for Mac so it works correctly with the Portuguese keyboard layout when connecting to a Windows 7 computer? I want to configure it to work the same way that the Apple keyboard is configured when using Windows 7 through Boot Camp.
All you need to do is to select the Portuguese keyboard layout in software on Mac OS X and also select the Portuguese keyboard layout on the Windows 7 computer to which you are connecting.
You can customize the keyboard behavior in the Preferences of Microsoft Remote Desktop Connection for Mac.
I'm not sure I fully understood your question.
An obvious answer is: Microsoft Remote Desktop Connection for Mac has a section Keyboard in its Preferences window. There you can configure the mapping for a few special keys such as the Windows "start" key.
I personally use an Apple Bluetooth keyboard (the recent model, without numeric keypad) on a Mac with which I frequently connect to a Windows 7-based PC through Remote Desktop Connection. But I've never felt the need to change the application's default keyboard mapping preference settings.
My apologies if this doesn't answer your question. Perhaps you want to have more control over the keyboard mapping? But this isn't clear to me from your original question.