<font face="Arial, Verdana">Just in case someone else is trying to do this...</font>
Turns out you can connect the two apps using a CURL script.
Basically you will need to install CURL. Then add this command to your "Starting Script" tab of your S3D Settings. (The same place where you specify Infill% , supports, materials, etc)
Replace the x-api-key value with the API value from your Repetier Server.
Replace the IP Address with the correct IP.
Replace the printer name with your printer name. (Mine is StuffMaker.)
To use, simply prepare your project as usual in S3D. Then select the save to SD card option. Save the gcode to any location, doesn't matter what folder. After it saves, you should see it uploaded directly to Repetier server.
It doesn't start automatically. (I wish it did). You will have to either click print on the touch screen, or on your computer via the web browser.
"curl.exe" -i -X POST -H "Content-Type: multipart/form-data" -H "x-api-key: f063f12a-198c-42fa-99af-529a5a745c339" -F "a=upload" -F "filename=@[output_filepath]" "
http://192.168.1.107:3344/printer/model/StuffMaker"</pre></div>