I never tried it myself but, from my experience, I can imagine two different workflows:

a) Using Ecosystem Paint feature (only available in V6). You do not click on "populate". You just paint your ecosystem in the visible top part of your object. Then you rotate the object and paint the ecosystem on the new top part. And so on, until everything is painted. That's really easy, I think. And you have precise control over what's painted.

b) If you dont have V6, you can click "populate". Then duplicate the object and rotate it, as many times as you need to cover everything. Finally, you make the base texture of the duplicated objects 100% transparent. This has the disadvantage of you getting equal patterns of the ecosystem, which, depending on your population, might become too noticeable. If this is the case, when you duplicate the object, you can click "clear" and "populate" again on the duplicated object. You might have to adjust the rotation in this case.

I haven't tried any of these methods but do drop me a PM if this works! I'd be interested to know! :-)