There is a script that will select open edges for you so you can boolean. I can't fish for it now because I'm at work but someone will probably post it for you.

Sometimes you have to scale your model down to a tenth of the size in order to meet boolean tolerances. It's a workaround that I hope goes away. I'd much rather have editable tolerances.

Lastly, I quit using the fillet tool and make my own with blends, lofts and stuff. It sounds like a lot of work (and I guess it can be) but you get total control over how the fillet ends up.

I came from the poly modeling world too. It took me a long time to readjust myself to the way surface modeling works. You'll get there. The best advice I can give is to slow down. Try some basic tutorials. It might seem like going backwards but when you learn to "think" in terms of surfaces you can really model so much more freely.