[Stiglr]

First lesson is: don't use Booleans! They're incredibly messy and ineffecient!! They often create much more of a mess than they're worth, and you'll spend more time cleaning up after them than you save with the so-called "instant operation".

The best strategy to make a smooth transition between intersecting cylindrical shapes is to use the knife tool to slice off areas that are "left inside" a joined unit. Then, add vertices on surface lines as necessary (by selecting vertices that flank the desired point and Create Vertice), then move them to the intersection point with another surface. Then join up points and weld. Or, where small "holes" are formed, create new surfaces at odd junctures, remembering to select vertices in succession, counterclockwise, before using Create Surface.

It's "manual" and it can be a little time consuming, but you're likely to get much better results than going for the quick fix supposedly afforded by the Boolean operations.