What's funny about bringing your own parts is that 3 guys here - trans/diff guy, exhaust/muffler guy, and my mechanic guy - usually suggest I do that.
Bear in mind that I do frequent business with them, and take care of them for stuff like racking the car for a look - $20 or a 12-pack of beer - and refer customers to them.
I communicate that I know they need a profit margin on parts, and often enough slide 'em either extra money or beers (beer is like clean money around here).
They know I'm fairly picky, but I pay whatever the bill is and don't grind them on cost or time...I figure it's just being respectful.
Bottom line is to establish a relationship with whoever works on your stuff, and things almost always go well, win/win.