At the moment using good naming conventions,groups and layers. Anything else I can to do manage this scene ? Also would using instances instead of duplicates for repeating objects make the file size smaller,scene run faster its got pretty slow. Are there any downsides to using them come render time ?
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You can also use charakters as references. For example you got a lowpoly proxy character with a rough skinning applied and when it comes to rendering the highpoly character with all the fancy materials and so on gets loaded by maya.
Scene Assembly is new and only appeared in the extension release of Maya 2013. I would definitely advise people to look into this feature. It's perhaps seen as the next logical step for referencing.
In terms of Naming convention, name it in a way that is easily selectable with select by name. Imagine if you have hundreds of barrels in the scene named as pcylinder and polysurface, it would be hard to select them all at once. It you name it all as "Barrel" you can easily select all of them at once. Im sure a lot people know this, but I think its worth mentioning cuz a lot of time ppl forget.
I had so many times where i recieved a scene from someone that things werent named properly. I had to go through the whole scene and select stuff one by one to rename stuff.