are you authoring it yourself? if yes, what software are you using? As for dolby, most of the editing software will allow you to encode to dobly surround (noting that you already laied the 6 channels correctly and ready to export it into ac3). Premiere Pro allows you 3 uses free befores you have to PAY for the license, FCP I think it's already incorporated, so is Vegas 6.
Most authoring software shouldn't have problem using ac3 audio and let you be listening in 5.1 surround, except for Ulead DVD Workshop 2.0, you have to be VERY careful not to do anything within the authoring software or it would ruin your 5.1 encoding (Ulead tends to 're-encode' your audio within if you have trimmed, change, adjusted the audio level or whatever of the video clip that has the ac3 file), you must and ONLy bring it in and play it back as it is. I know casue I had a 4 days nightmare back then when encoding A Joker's Card until finally I learned what needed to be done to have Ulead DVD Workshop 2 keep my ac3 file intact.