I am able to correctly route and map channels in Premiere and audition, that really isn't the problem. The issue arises in how Voukoder assigns the channels upon export. After doing some extensive testing with exporting several different configurations I realized Voukoder no matter what exports the channel scheme as you mentioned above L, R, C, LFE, Ls, Rs. It does not matter how you arrange your tracks on the timeline Voukoder will export it this way. Perhaps this information will help some poor soul having the same issues I was having.
But this works for me wonderfully now and sounds great on my surround sound system using Plex for playback. 2 small details to point out that may save someone the same headaches I had. In Premiere itself before you open the Voukoder tab make sure in the audio tab that audio is set to 5.1 as you mentioned above. And within Voukoder select AAC (FFMPEG) audio and within the options make sure you select "low complexity" I kept having problems when the profile was set to main or anything else but once I tried low complexity it worked like a charm.
The other little detail is Premiere and Voukoder only allow a 5.1 export. So what do you do with a 7.1 mix? Well all I did was take those alternate left and right surround channels and routed them to the main left and right surround channels. I tested it out and it worked just fine. I could hear both mixed properly.