The antennas will not effect whether or not you get DD5.1 audio.
First off the DD5.1 audio will only be available on the all digital HDTV broadcasts. So you will need a HDTV ATSC tuner to receive your OTA digital station. Next you will have to make sure to use a digital connection between your ATSC tuner and the Yamaha receiver. This can be either a Toslink or SPIDF digital coax cable. Finally make sure that your tuner is properly configured.
I know of some Cable boxes which default to "stereo" instead of "matrix". Matrix enables DD5.1 on that particular box.
You ask about which stations broadcast DD5.1. Well FOX, WB and ABC do. CBS and NBC sometimes do. With that said, sometimes a local station does not broadcast DD5.1 even though the network supports it. You will have to check with other HDTV users in your area to see into this.