When rendering and uploading your sequence, you have the option to select a predefined rendering option labeled "Select preset file...". This is best used when you need a custom frame format or different codecs. This option opens a file dialog that asks for an Adobe Media Encoder preset file (.epr) file.
Here is how you create one:
Creating a Media Encoder preset file (.epr)
Open Adobe Media Encoder
Click the "Create New Preset" button as shown below
Change the preset settings, Enter a Preset Name and then click OK.
Your newly created preset is now listed under "User Presets & Groups." Select the preset and click the "Export Presets" button
You have now created an .epr preset file that you can use to render and upload your sequence.
Importing timecode with a custom preset
Importing the timecode is done within the custom preset. Under Preset Settings at the bottom, you will see the option to select Set Start Timecode. Check this box and enter the starting timecode.