Many of the machines have multiple output slots. While I know many different ways to selective remove what I want. I was wondering what the intended method was. I want to write up a tutorial for my community to use, but I want to state the intended method of selective removing the stuff instead of tying it to the mods i just happen to use.

Heyo! There isn't really a special 'intended' method as such. All sides are available to extract from, so you can use whichever sides you want. If you don't have enough sides to work with, then connecting a 'machine interface' is an option, giving more sides to work with :)

what I meant was if there are 4 outputs (such as the centrifuge) how do you select the top right tank without emptying the top left first? or empty a tank that doesn't have exactly 1000 mb. Again I know ways to do this, but was just checking there wasn't an item or method in the mod I was overlooking.

Yeh, again, there's no particular method. It doesn't necessarily have to be a bucket that you use to interact with the fluids in machines - any fluid holder will do.

And the way pipes extract the fluid is not up to me, but up to how the other mod has its pipes implemented. Some mods have pipes which can skip over, say, the top left fluid with a filter, such as BC, where others such as TD can't.