[Stiglr]

As to the handle, it's hard to tell what's "messy" about it without seeing it. Post a screenshot and perhaps we can help you.

As to making a hole in a box or cylinder... there are a variety of ways to do that, too. I depends on what shape the hole is... and it depends on the object that you're cutting it out of.

Perhaps the best way to do it might be to simply create a set of vertices that represent the edge of your hole... move them in proper proximity to the outer surface of the object you want to place the hole in... then remove the surfaces of the object surface, and in vertice mode, recreate that outer surface using the vertices of the hole... (hard to describe in words)

Or... you can use objects and the Knife tool to better describe the hole, then just eliminate the polys of the hole once you've isolated them in the structure of the object you're making the hole in (again, ard to describe in words)


There are two, more "automatic" ways to do this, but depending on a number of factors they might not work with the objects you describe, or might be very messy in terms of the "damage" done to the object you cut the hole out of.

These are "Make Hole" and "Boolean Cut".