Export your 5.1 surroundmix as 6 individual WAV monofiles or just one multichannel WAV from your favorite program. Then encode your AC3 with WAV to AC3 Encoder (It’s freeware). https://thefrontend.sourceforge.net
It gives you a perfect 5.1 Dolby Surround .ac3 file ready to drag and drop into Encore.
WAV to AC3 Encoder is a GUI for Aften A/52 audio encoder created by Justin Ruggles. WAV to AC3 Encoder can encode multi-channel WAV files and/or multiple mono WAV files into AC-3 audio files.
WAV to AC3 Encoder project was started at 27 January 2007 by Wiesław Šoltés. There are Win32 (x86) and x64 (x86_64, AMD64) binaries available. WAV to AC3 Encoder fully supports UNICODE and ANSI. This program is very fast with full support of multi-core and multi-cpu machines (you can do detailed benchmarks using logging function).
Supported operating systems: Miscrosoft Windows 98SE, Me, XP, XP 64bit, 2003, 2003 64bit, Vista, Vista 64bit, 2008, 2008 64bit.
The main developer of WAV to AC3 Encoder is Wiesław Šoltés (wiso, wisodev).