Hi steve

The better / cleaner your models are the easier they are to output.

A couple of quick tips (ignore if you know this already or it is too far back to basics)

When you select an object it will say up the top right hand corner (solid) which is usually pretty good
If it changes to a "joined surface" at any point I start looking for reasons and backing up.

To get clean results you will find that when cutting solids (boolean difference) either with another solid or a surface it pays to have some overlap where the cutting object goes beyond the outside surface of the solid.
If the cutting object is flush with the surface it often leaves a messy surface or the solid becomes a joined surface which will not print.

If you find when joining 2 solids (union) and you see they go from 2 or 3 solids to a joined surface you can back up (ctrl Z) and either move 1 solid slightly or scale it slightly (even .5% can be enough) and try the union again, often this will work.

Also I find that rather then join 20 solids at once, select 2 or 3 at a time which will often union then add the next ones, then next etc untill done.

If you use booleen difference rather than chamfer to angle an area or shape a surface you can control the result more

For example with the following bezel



If you camfer the inside edges you get



whereas using a cutting solid that goes beyond the surface (made by rail revolving an angled line to form the cutting solid)



As you can see you get a much cleaner inside chamfer.



Some of this stuff can take months of trial an error to figure out

But when it all goes wrong and will take hours to backtrack or redesign and you find some bad edges or faces that are just too difficult and time consuming to find or fix (I know purists will cringe)

there is a great service on line that you can upload your stl model to for repair, then download it back

http://cloud.netfabb.com/index.php

I use a program called minimagics 2.0 to check my models if it gives you the OK you can guarantee it will print.
Which comes from Materialise who is the company featured at the top of this post by fabien

cheers
shayne