Headroom wrote:... I would say that often built-in functions of 3D applications are mostly affecting only their internal render engines.
Exactomundo, this was also the mistake here!
Headroom wrote:Material settings that are for the internal render engine may not automatically translate into anything useable for the exporter and you may have to redefine the materials again using the exporter's functions.
Cindigo does a "on-the-fly-indigo-translation" of the C4D materials, but it is not perfect and won't be! So you end up with the need for Indigo materials anyway ...
avp216 wrote:1. A sky (Created using the built in function of... Create a sky

First mistake! You define a Sky, HDRI or background whatever via "Indigo Advanced Options" in der C4D Render Settings.
Just add it like you would Add Ambient Occlusion to a scene.
avp216 wrote:2. A floor (With a material placed on top to mimic the ocean (bump map, etc)
This actually could work with a plane (normals up) and the correct Specular material with IOR @ 1.32 or even better a SSS water material from the Mat DB.
avp216 wrote:3. Clouds (once again, using the built in function.
Nope, no clouds availible for Indigo atm!
avp216 wrote:I tried rendering it with indigo, but the only thing that appeared to be rendered was the sky.. no cloud, no ocean, no nothing. just a blue sky.
Cindigo doesn't export the C4D "Ground" Object (you used for the water)
avp216 wrote:I added a glowing material to an object, but yet, it doesn't glow in indigo.
Do you even use Indigo materials?? You create them go in the C4D Materials overview on the Bottom and there "File > Create new Indigo Material"
The Cindigo Manual explains all that very nicely and the Cindigo Tutorial gives insight to the very first steps, get both here:
http://www.indigorenderer.com/documentation/cinema4d