In Maya, there are snap align tools (1-Point, 2-Point, 3-Point) that make this sort of thing super-easy and precise. Not sure if Max has an analogous tool, but you may want to look around for something similar. Maybe a plug-in or something.
In this example, I would combine all the cylinders into an object, just as you did. But instead of quickslice (Cut Face Tool in Maya), I would select 3 adjacent vertices from one end of one of the cylinders (representing the plane I'm trying to align) and then 3 of the 4 vertices that comprise the empty rectangle. Then I'd run the 3-Point Snap Align tool to perfectly align the multi-cylinder object to the main object.
This gives you unskewed circles that are perfectly in-line with whatever arbitrarily oriented flat surface you need to poke holes into. Although, I would advise people to only make simple indentations like holes when it's absolutely necessary. If the effect you're trying to achieve can be done via texture/bump/normal/displacement and doesn't change the contour of your model, don't bother modelling it in unless you're using Mudbox or Z-brush.
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