Check out "How to use the new rectangular bottle" under the instructions tab of this page: http://shop.inkjetmall.com/ConeColor-Pro-K3-ink-220ml-Set-of-9.html
I, too, tried what you were doing with the nipple on the new style bottles.
I believe the little nipples are for priming the cartridges if they cannot be primed using the vacuum method. This can occur if a cart runs dry for some reason. But, on an R3000, you really don't want to run a cart dry. Youl'll have to run an ink charge cycle which uses a lot of ink to charge one line.
I'll agree that instructions tend to be scattered about. I'm not sure if IJM is including paper instructions anymore, or if they have the instructions for using the nipples on the bottles. I do know they're working on consolidating and organizing information.